Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Santangelo, Brook E.; Apgar, Madison; Colorado, Angela Burkhart; Martin, Casey G.; Sterrett, John; Wall, Elena; Joachimiak, Marcin P.; Hunter, Lawrence E.; Lozupone, Catherine A.

doi:10.3389/fmicb.2024.1351678

Title: Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Journal Article · Thu Apr 04 00:00:00 UTC 2024 · Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2024.1351678 · OSTI ID:2470750

Santangelo, Brook E. ^[1]; Apgar, Madison ^[1]; Colorado, Angela Burkhart ^[1]; Martin, Casey G. ^[1]; Sterrett, John ^[2]; Wall, Elena ^[1]; Joachimiak, Marcin P. ^[3]; Hunter, Lawrence E. ^[1]; Lozupone, Catherine A. ^[1]

University of Colorado, Aurora, CO (United States). School of Medicine
Univ. of Colorado, Boulder, CO (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC02-06CH11357; AC02-98CH10886; AC05-00OR22725

OSTI ID:: 2470750

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 15; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (105)

Predicting the relationships between gut microbiota and mental disorders with knowledge graphs Liu, Ting; Pan, Xueli; Wang, Xu Health Information Science and Systems, Vol. 9, Issue 1 https://doi.org/10.1007/s13755-020-00128-2	journal	November 2020
Short-chain fatty acid metabolism and multiple effects on cardiovascular diseases Hu, Tongtong; Wu, Qingqing; Yao, Qi Ageing Research Reviews, Vol. 81 https://doi.org/10.1016/j.arr.2022.101706	journal	November 2022
Fingerprint profiling and gut microbiota regulation of polysaccharides from Fritillaria species Wei, Wenlong; Li, Zhenwei; Li, Shiwei International Journal of Biological Macromolecules, Vol. 237 https://doi.org/10.1016/j.ijbiomac.2023.123844	journal	May 2023
Microbiome and metabolome data integration provides insight into health and disease Shaffer, Michael; Armstrong, Abigail J. S.; Phelan, Vanessa V. Translational Research, Vol. 189 https://doi.org/10.1016/j.trsl.2017.07.001	journal	November 2017
Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome Esvap, Elif; Ulgen, Kutlu O. ACS Synthetic Biology, Vol. 10, Issue 9 https://doi.org/10.1021/acssynbio.1c00140	journal	August 2021
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn Nature Biotechnology, Vol. 29, Issue 5 https://doi.org/10.1038/nbt.1823	journal	May 2011
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura Nature Biotechnology, Vol. 35, Issue 1 https://doi.org/10.1038/nbt.3703	journal	November 2016
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis Sung, Jaeyun; Kim, Seunghyeon; Cabatbat, Josephine Jill T. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15393	journal	June 2017
Metabolomics: beyond biomarkers and towards mechanisms Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary Nature Reviews Molecular Cell Biology, Vol. 17, Issue 7 https://doi.org/10.1038/nrm.2016.25	journal	March 2016
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms Wallen, Zachary D.; Demirkan, Ayse; Twa, Guy Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-34667-x	journal	November 2022
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine Heinken, Almut; Hertel, Johannes; Acharya, Geeta Nature Biotechnology, Vol. 41, Issue 9 https://doi.org/10.1038/s41587-022-01628-0	journal	January 2023
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures Geistlinger, Ludwig; Mirzayi, Chloe; Zohra, Fatima Nature Biotechnology, Vol. 42, Issue 5 https://doi.org/10.1038/s41587-023-01872-y	journal	September 2023
Reporting guidelines for human microbiome research: the STORMS checklist Mirzayi, Chloe; Renson, Audrey; Furlanello, Cesare Nature Medicine, Vol. 27, Issue 11 https://doi.org/10.1038/s41591-021-01552-x	journal	November 2021
Qiita: rapid, web-enabled microbiome meta-analysis Gonzalez, Antonio; Navas-Molina, Jose A.; Kosciolek, Tomasz Nature Methods, Vol. 15, Issue 10 https://doi.org/10.1038/s41592-018-0141-9	journal	October 2018
Learning representations of microbe–metabolite interactions Morton, James T.; Aksenov, Alexander A.; Nothias, Louis Felix Nature Methods, Vol. 16, Issue 12 https://doi.org/10.1038/s41592-019-0616-3	journal	November 2019
Protein ontology on the semantic web for knowledge discovery Chen, Chuming; Huang, Hongzhan; Ross, Karen E. Scientific Data, Vol. 7, Issue 1 https://doi.org/10.1038/s41597-020-00679-9	journal	October 2020
Towards a knowledge graph for pre-/probiotics and microbiota–gut–brain axis diseases Liu, Ting; Lan, Gongjin; Feenstra, K. Anton Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-21735-x	journal	November 2022
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals Carbonell, Pablo; Jervis, Adrian J.; Robinson, Christopher J. Communications Biology, Vol. 1, Issue 1 https://doi.org/10.1038/s42003-018-0076-9	journal	June 2018
The human microbiome in health and disease: hype or hope Falony, Gwen; Vandeputte, Doris; Caenepeel, Clara Acta Clinica Belgica, Vol. 74, Issue 2 https://doi.org/10.1080/17843286.2019.1583782	journal	February 2019
A deep learning method for predicting metabolite–disease associations via graph neural network Sun, Feiyue; Sun, Jianqiang; Zhao, Qi Briefings in Bioinformatics, Vol. 23, Issue 4 https://doi.org/10.1093/bib/bbac266	journal	July 2022
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver Bioinformatics, Vol. 28, Issue 14 https://doi.org/10.1093/bioinformatics/bts252	journal	May 2012
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies Jackson, Rebecca; Matentzoglu, Nicolas; Overton, James A. Database, Vol. 2021 https://doi.org/10.1093/database/baab069	journal	October 2021
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Cantalapiedra, Carlos P.; Hernández-Plaza, Ana; Letunic, Ivica Molecular Biology and Evolution, Vol. 38, Issue 12 https://doi.org/10.1093/molbev/msab293	journal	October 2021
The Protein Information Resource (PIR) Barker, W. C. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.41	journal	January 2000
COG database update: focus on microbial diversity, model organisms, and widespread pathogens Galperin, Michael Y.; Wolf, Yuri I.; Makarova, Kira S. Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1018	journal	November 2020
GenBank Sayers, Eric W.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1023	journal	November 2020
WikiPathways: connecting communities Martens, Marvin; Ammar, Ammar; Riutta, Anders Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1024	journal	November 2020
BRENDA, the ELIXIR core data resource in 2021: new developments and updates Chang, Antje; Jeske, Lisa; Ulbrich, Sandra Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1025	journal	November 2020
The Human Phenotype Ontology in 2021 Köhler, Sebastian; Gargano, Michael; Matentzoglu, Nicolas Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1043	journal	December 2020
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes Seaver, Samuel M. D.; Liu, Filipe; Zhang, Qizhi Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa746	journal	September 2020
GIMICA: host genetic and immune factors shaping human microbiota Tang, Jing; Wu, Xianglu; Mou, Minjie Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa851	journal	October 2020
Ensembl 2021 Howe, Kevin L.; Achuthan, Premanand; Allen, James Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa942	journal	November 2020
The international nucleotide sequence database collaboration Arita, Masanori; Karsch-Mizrachi, Ilene; Cochrane, Guy Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa967	journal	November 2020
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models Moretti, Sébastien; Tran, Van Du T.; Mehl, Florence Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa992	journal	November 2020
Rhea, the reaction knowledgebase in 2022 Bansal, Parit; Morgat, Anne; Axelsen, Kristian B. Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1016	journal	November 2021
HMDB 5.0: the Human Metabolome Database for 2022 Wishart, David S.; Guo, AnChi; Oler, Eponine Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1062	journal	November 2021
The Human Disease Ontology 2022 update Schriml, Lynn M.; Munro, James B.; Schor, Mike Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1063	journal	November 2021
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy Parks, Donovan H.; Chuvochina, Maria; Rinke, Christian Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab776	journal	September 2021
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites Cheng, Liang; Qi, Changlu; Yang, Haixiu Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab786	journal	September 2021
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR Olson, Robert D.; Assaf, Rida; Brettin, Thomas Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1003	journal	November 2022
UniProt: the Universal Protein Knowledgebase in 2023 Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1052	journal	November 2022
MiMeDB: the Human Microbial Metabolome Database Wishart, David S.; Oler, Eponine; Peters, Harrison Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac868	journal	October 2022
ChemFOnt: the chemical functional ontology resource Wishart, David S.; Girod, Sagan; Peters, Harrison Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac919	journal	October 2022
PubChem 2023 update Kim, Sunghwan; Chen, Jie; Cheng, Tiejun Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac956	journal	October 2022
InterPro in 2022 Paysan-Lafosse, Typhaine; Blum, Matthias; Chuguransky, Sara Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac993	journal	November 2022
The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods Zdrazil, Barbara; Felix, Eloy; Hunter, Fiona Nucleic Acids Research, Vol. 52, Issue D1 https://doi.org/10.1093/nar/gkad1004	journal	November 2023
Achieving pan-microbiome biological insights via the dbBact knowledge base Amir, Amnon; Ozel, Eitan; Haberman, Yael Nucleic Acids Research, Vol. 51, Issue 13 https://doi.org/10.1093/nar/gkad527	journal	June 2023
The PEDANT genome database Frishman, D. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg005	journal	January 2003
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Boeckmann, B. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg095	journal	January 2003
The Unified Medical Language System (UMLS): integrating biomedical terminology Bodenreider, O. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh061	journal	January 2004
BLAST: at the core of a powerful and diverse set of sequence analysis tools McGinnis, S.; Madden, T. L. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh435	journal	July 2004
Entrez Gene: gene-centered information at NCBI Maglott, D.; Ostell, J.; Pruitt, K. D. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl993	journal	January 2007
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics Cantarel, B. L.; Coutinho, P. M.; Rancurel, C. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn663	journal	January 2009
The NCBI Taxonomy database Federhen, S. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1178	journal	December 2011
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
BacDive—the Bacterial Diversity Metadatabase Söhngen, Carola; Bunk, Boyke; Podstawka, Adam Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1058	journal	November 2013
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database Jewison, Timothy; Su, Yilu; Disfany, Fatemeh Miri Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1067	journal	November 2013
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks Yilmaz, Pelin; Parfrey, Laura Wegener; Yarza, Pablo Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1209	journal	November 2013
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
ChEBI in 2016: Improved services and an expanding collection of metabolites Hastings, Janna; Owen, Gareth; Dekker, Adriano Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1031	journal	October 2015
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1189	journal	November 2015
KEGG: new perspectives on genomes, pathways, diseases and drugs Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1092	journal	November 2016
DrugBank 5.0: a major update to the DrugBank database for 2018 Wishart, David S.; Feunang, Yannick D.; Guo, An C. Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1037	journal	November 2017
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics Wittig, Ulrike; Rey, Maja; Weidemann, Andreas Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1065	journal	October 2017
The Reactome Pathway Knowledgebase Fabregat, Antonio; Jupe, Steven; Matthews, Lisa Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1132	journal	November 2017
The Gene Ontology Resource: 20 years and still GOing strong Nucleic Acids Research, Vol. 47, Issue D1, p. D330-D338 https://doi.org/10.1093/nar/gky1055	journal	November 2018
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1085	journal	November 2018
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie Nucleic Acids Research, Vol. 46, Issue 15 https://doi.org/10.1093/nar/gky537	journal	June 2018
Protein Data Bank: the single global archive for 3D macromolecular structure data Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky949	journal	October 2018
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease Noronha, Alberto; Modamio, Jennifer; Jarosz, Yohan Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky992	journal	October 2018
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree Norsigian, Charles J.; Pusarla, Neha; McConn, John Luke Nucleic Acids Research https://doi.org/10.1093/nar/gkz1054	journal	November 2019
BioModels—15 years of sharing computational models in life science Malik-Sheriff, Rahuman S.; Glont, Mihai; Nguyen, Tung V. N. Nucleic Acids Research https://doi.org/10.1093/nar/gkz1055	journal	November 2019
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life Mendler, Kerrin; Chen, Han; Parks, Donovan H. Nucleic Acids Research, Vol. 47, Issue 9 https://doi.org/10.1093/nar/gkz246	journal	April 2019
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions Cheng, Liang; Qi, Changlu; Zhuang, He Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz843	journal	October 2019
PathBank: a comprehensive pathway database for model organisms Wishart, David S.; Li, Carin; Marcu, Ana Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz861	journal	October 2019
The MetaCyc database of metabolic pathways and enzymes - a 2019 update Caspi, Ron; Billington, Richard; Keseler, Ingrid M. Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz862	journal	October 2019
Mondo: Unifying diseases for the world, by the world Vasilevsky, Nicole A.; Matentzoglu, Nicolas A.; Toro, Sabrina https://doi.org/10.1101/2022.04.13.22273750	preprint	May 2022
Ontologies in Biological Data Visualization Carpendale, Sheelagh; Evanko, Daniel IEEE Computer Graphics and Applications, Vol. 34, Issue 2 https://doi.org/10.1109/MCG.2014.33	journal	March 2014
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science Unni, Deepak R.; Moxon, Sierra A. T.; Bada, Michael Clinical and Translational Science, Vol. 15, Issue 8 https://doi.org/10.1111/cts.13302	journal	June 2022
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species Gillespie, Joseph J.; Wattam, Alice R.; Cammer, Stephen A. Infection and Immunity, Vol. 79, Issue 11 https://doi.org/10.1128/IAI.00207-11	journal	September 2011
GapMind: Automated Annotation of Amino Acid Biosynthesis Price, Morgan N.; Deutschbauer, Adam M.; Arkin, Adam P. mSystems, Vol. 5, Issue 3 https://doi.org/10.1128/mSystems.00291-20	journal	June 2020
A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome Armour, Courtney R.; Nayfach, Stephen; Pollard, Katherine S. mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/mSystems.00332-18	journal	May 2019
Systems Analysis of Gut Microbiome Influence on Metabolic Disease in HIV-Positive and High-Risk Populations Armstrong, Abigail J. S.; Quinn, Kevin; Fouquier, Jennifer mSystems, Vol. 6, Issue 3 https://doi.org/10.1128/mSystems.01178-20	journal	June 2021
Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries Ghosh, Tarini Shankar; Rampelli, Simone; Jeffery, Ian B. Gut, Vol. 69, Issue 7 https://doi.org/10.1136/gutjnl-2019-319654	journal	February 2020
Resource description framework: metadata and its applications Candan, K. Selçuk; Liu, Huan; Suvarna, Reshma ACM SIGKDD Explorations Newsletter, Vol. 3, Issue 1 https://doi.org/10.1145/507533.507536	journal	July 2001
The pathway ontology – updates and applications Petri, Victoria; Jayaraman, Pushkala; Tutaj, Marek Journal of Biomedical Semantics, Vol. 5, Issue 1 https://doi.org/10.1186/2041-1480-5-7	journal	January 2014
Relations in biomedical ontologies Smith, Barry; Ceusters, Werner; Klagges, Bert Genome Biology, Vol. 6, Issue 5, p. R46 https://doi.org/10.1186/gb-2005-6-5-r46	journal	January 2005
Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome Le, Vuong; Quinn, Thomas P.; Tran, Truyen BMC Genomics, Vol. 21, Issue S4 https://doi.org/10.1186/s12864-020-6652-7	journal	July 2020
Disbiome database: linking the microbiome to disease Janssens, Yorick; Nielandt, Joachim; Bronselaer, Antoon BMC Microbiology, Vol. 18, Issue 1 https://doi.org/10.1186/s12866-018-1197-5	journal	June 2018
ICD-11: an international classification of diseases for the twenty-first century Harrison, James E.; Weber, Stefanie; Jakob, Robert BMC Medical Informatics and Decision Making, Vol. 21, Issue S6 https://doi.org/10.1186/s12911-021-01534-6	journal	November 2021
A systematic assessment of current genome-scale metabolic reconstruction tools Mendoza, Sebastián N.; Olivier, Brett G.; Molenaar, Douwe Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1769-1	journal	August 2019
OHMI: the ontology of host-microbiome interactions He, Yongqun; Wang, Haihe; Zheng, Jie Journal of Biomedical Semantics, Vol. 10, Issue 1 https://doi.org/10.1186/s13326-019-0217-1	journal	December 2019
Microbiome definition re-visited: old concepts and new challenges Berg, Gabriele; Rybakova, Daria; Fischer, Doreen Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00875-0	journal	June 2020
MiMeNet: Exploring microbiome-metabolome relationships using neural networks Reiman, Derek; Layden, Brian T.; Dai, Yang PLOS Computational Biology, Vol. 17, Issue 5 https://doi.org/10.1371/journal.pcbi.1009021	journal	May 2021
biochem4j: Integrated and extensible biochemical knowledge through graph databases Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0179130	journal	July 2017
Baseline human gut microbiota profile in healthy people and standard reporting template King, Charles H.; Desai, Hiral; Sylvetsky, Allison C. PLOS ONE, Vol. 14, Issue 9 https://doi.org/10.1371/journal.pone.0206484	journal	September 2019
Functional Distribution of Bacterial Community under Different Land Use Patterns Based on FaProTax Function Prediction Liang, Shichun; Deng, Jiaojiao; Jiang, Yong Polish Journal of Environmental Studies, Vol. 29, Issue 2 https://doi.org/10.15244/pjoes/108510	journal	January 2020
Systematized Nomenclature of Medicine–Clinical Terminology (SNOMED CT) Clinical Use Cases in the Context of Electronic Health Record Systems: Systematic Literature Review Vuokko, Riikka; Vakkuri, Anne; Palojoki, Sari JMIR Medical Informatics, Vol. 11 https://doi.org/10.2196/43750	journal	February 2023
MDAD: A Special Resource for Microbe-Drug Associations Sun, Ya-Zhou; Zhang, De-Hong; Cai, Shu-Bin Frontiers in Cellular and Infection Microbiology, Vol. 8 https://doi.org/10.3389/fcimb.2018.00424	journal	December 2018
Amadis: A Comprehensive Database for Association Between Microbiota and Disease Li, Long; Jing, Qingxu; Yan, Sen Frontiers in Physiology, Vol. 12 https://doi.org/10.3389/fphys.2021.697059	journal	July 2021
Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data Passi, Anurag; Tibocha-Bonilla, Juan D.; Kumar, Manish Metabolites, Vol. 12, Issue 1 https://doi.org/10.3390/metabo12010014	journal	December 2021

Similar Records

The INE-Beamline for Actinide Research at ANKA

Journal Article · Fri Feb 02 04:00:00 UTC 2007 · AIP Conference Proceedings · OSTI ID:21054765

Brendebach, Boris; Denecke, Melissa A; Rothe, Joerg; +2 more

Intraatomic correlation correction in the FORS model

Journal Article · Thu May 23 04:00:00 UTC 1985 · J. Phys. Chem.; (United States) · OSTI ID:5133773

Lam, B; Schmidt, M W; Ruedenberg, K

A Perturbative Solution for Nonlinear Stratified Upwelling over a Frictional Slope

Journal Article · Sun Oct 01 04:00:00 UTC 2023 · Journal of Physical Oceanography · OSTI ID:2580152

Choi, Jang-Geun; Pringle, James; Lippmann, Thomas

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
computational biology
databases
inference
microbiology
microbiome
ontologies

Title: Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Citation Formats

References (105)

Similar Records

Related Subjects