Table 3 List of all the data that was utilized in the microbe–disease prediction
From: In-silico computational approaches to study microbiota impacts on diseases and pharmacotherapy
Data | Source | Original state | Similarity process | URL |
|---|---|---|---|---|
HMDAD | The HMDAD database provides documentation of population disorders of disease-related microorganisms in PubMed | HMDAD integrated 483 disease-microbe entries which include 39 diseases and 292 microbes | They're reduced to 450 known MDAs that are then utilized to calculate GIP kernel, Cosine, and Spearman correlation similarity | |
PERYTON | The content of Peryton is entirely supported by the manual curation of biomedical journals. Using reference tools to construct database dictionaries, diseases and Microbiota are supplied in a well-structured, well-organized format | There are currently over 7,900 entries in the database, which link 43 diseases and 1,396 microorganisms | Peryton also provides interactive visualizations, and the data may be downloaded straight to your computer for local storage and analysis | |
GEN-BASED | On DisGeNET, you may find GDAs from UNIPROT, CGI, ClinGen, Genomics England, CTD (human subset), PsyGeNET, Orphanet, and those produced from text mining MEDLINE abstracts | Between 17 549 genes and 24 166 diseases, there are 628 685 GDAs covered. There are 37 diseases mapped, 1850 chromosomes, and 2715 GDAs Size/coverage in HMDAD | The neighbor-based similarity approach calculates GDA scores which were used to find further commonalities among a selection of disorders | |
SYMPTOM-BASED disease data | HSDN pulls data from PubMed's large-scale medical bibliographic records of disease–symptom correlations | Simultaneous counting and TF-IDF weight values for 322 symptoms and 4442 disorders, with 147 97 connections and 22 mapped diseases, 269 symptoms, and 1858 associations of disease symptoms | The symptom-based illness similarity is calculated using Co-occurrence TF-IDFs between one illness and other symptoms | |
Semantics-based disease data | MeSH trees are in the National Library of Medicine for a hierarchical definition of disease | Hierarchical trees systematically describe a variety of diseases 33 diseases of size/coverage mapped in HMDAD | The DAG-based semantic similarity of two disease trees made up of hierarchical descriptors is calculated | |
PROTEIN | STRING is a database that collects protein–protein interactions and data on proteins from several sources | At the species level, 1391 microbes were mapped, with gene neighbor scores of 932 370 pairs of COGs | The neighborhood score is used to determine if there is an edge between two COGs. Also provides interactive visualizations | |
Comprehensive Antibiotic Resistance Database (CARD) | A carefully curated resource offering high-quality reference material on the molecular basis of antimicrobial resistance (AMR), with a focus on the genes, proteins, and mutations implicated in AMR | CARD found 2441 model reference sequences, 853 single nucleotide alterations, as well as an increasing number of indels, frame shift, and nonsense mutations linked to antimicrobial resistance | Additional search criteria include mutations conferring AMR (if relevant) and curated BLAST(P/N) bit score cut-offs are included in the ontology | |
Disbiome | Created in 2018, is a more comprehensive database that is constantly updated every three months | As of December 2019, the Disbiome database includes 322 diseases, 1,470 microbiome organisms, and 9,102 experiments published in 1,018 scholarly articles | The human annotation guarantees a clear and organized presentation of the material that is accessible | |
MicroPhenoDB | There are 5677 non-redundant correlations between 1781 microorganisms and 542 human illness phenotypes across more than 22 human body locations in this study | In addition, MicroPhenoDB has 696,934 connections between 27,277 clade-specific core genes and 685 microorganisms | The software allows scientists to search DNA and RNA sequences for potential pathogens without running the usual meta-genomic data processing and assembly steps |