Thank you for using the CMAUP database. Detailed data content (column names) of download files are listed below: ========================================================================================= ====="CMAUPv2.0_download_Plants": Plant_ID: Plant ID in CMAUP database Plant_Name: Plant Latin name Species_Tax_ID: NCBI Taxonomy ID at Species level Species_Name: Latin name at Species level Genus_Tax_ID: NCBI Taxonomy ID at Genus level Genus_Name: Latin name at Genus level Family_Tax_ID: NCBI Taxonomy ID at Family level Family_Name: Latin name of plant Family ========================================================================================= ====="CMAUPv2.0_download_ingredients_All" and "CMAUPv1.0_download_ingredients_onlyActive": Ingredient_ID: ingredient ID in CMAUP database pref_name: common name of ingredient iupac_name: IUPAC name of ingredient chembl_id: ingredient ID in ChEMBL database pubchem_cid: ingredient ID in PubChem database MW: molecular weight of ingredient LogS: LogS of ingredient (calculated using ADMETlab 2.0 software) LogD: LogD of ingredient (calculated using ADMETlab 2.0 software) LogP: LogP of ingredient (calculated using ADMETlab 2.0 software) nHA: number of hydrogen bond acceptor of ingredient (calculated using ADMETlab 2.0 software) nHD: number of hydrogen bond donor of ingredient (calculated using ADMETlab 2.0 software) TPSA: polar surface area of ingredient (calculated using ADMETlab 2.0 software) nRot: number of rotatable bond of ingredient (calculated using ADMETlab 2.0 software) nRing: number of rings of ingredient (calculated using ADMETlab 2.0 software) InChI: standard InCHI of ingredient InChIKey: standard InCHIKEY of ingredient SMILES: canonical SMILES of ingredient ========================================================================================= ====="CMAUPv2.0_download_Targets": Target_ID: target ID in CMAUP database Gene_Symbol: gene symbol of target Protein_Name: protein name of target Uniprot_ID: protein ID in UniPort database ChEMBL_ID: target ID in ChEMBL database TTD_ID: target ID in TTD database (Therapeutic Target Database) if_DTP: whether the target is defined as drug transporter (according to DrugMAP) if_CYP: whether the target is defined as Cytochromes P450 (according to DrugMAP) if_therapeutic_target: other therapeutic targets that don't belong to DTP and CYP Target_Class_Level1: protein class Target_Class_Level2: protein class Target_Class_Level3: protein class Target_Class_level_displayed: the most specific protein class from L1 to L3 was selected and displayed Target_type: type of target according to DrugMAP ========================================================================================= ====="CMAUPv2.0_download_Plant_Ingredient_Associations_allIngredients" and "CMAUPv1.0_download_Plant_Ingredient_Associations_onlyActiveIngredients": Plant_ID: plant ID in CMAUP database Ingredient_ID: ingredient ID in CMAUP database ========================================================================================= ====="CMAUPv2.0_download_Ingredient_Target_Associations_ActivityValues_References": Ingredient_ID: ingredient ID in CMAUP database Target_ID: target ID in CMAUP database Activity_Type: type of the activity record, e.g., IC50, EC50 Activity_Relationship: activity record relationship, e.g., <, = Activity_Value: exact value of the activity record Activity_Unit: unit of the activity record Reference_ID: ID of the reference where the activity record was reported Reference_ID_Type: type of reference ID, e.g., PMID (document ID in PubMed) ========================================================================================= ====="CMAUPv2.0_download_Human_Oral_Bioavailability_information_of_Ingredients_All": Ingredient_ID: ingredient ID in CMAUP database SMILES: canonical SMILES of ingredient XLOGP3: XLOGP3 of ingredient (calculated by RDKit and then evaluated using criteria from SwissADME) RTB: number of rotatable bound of ingredient (calculated by RDKit and then evaluated using criteria from SwissADME) TPSA: polar surface area of ingredient (calculated by RDKit and then evaluated using criteria from SwissADME) Fcsp3: the fraction of sp3 carbon atoms (calculated by RDKit and then evaluated using criteria from SwissADME) MW: molecular weight of ingredient ESOL: Estimated SOLubility of ingredient (calculated referring to the formula from the original paper: Delaney, John S. "ESOL: estimating aqueous solubility directly from molecular structure." Journal of chemical information and computer sciences 44.3 (2004): 1000-1005.) Prediction_HobPre: label predicted by HobPre. The original result was a float ranged from 0 to 1, which represent the probability of being high human oral bioavailability. Here we transformed the labels < 0.50 to be 0, and labels > 0.50 to be 1. Prediction_SwissADME: six descriptors are used by SwissADME to evaluate the oral bioavailability of a natural product: ☑ LIPO(Lipophility): -0.7 < XLOGP3 < +5.0 ☑ SIZE: 150g/mol < MW < 500g/mol ☑ POLAR(Polarity): 20Ų < TPSA < 130Ų ☑ INSOLU(Insolubility): -6 < Log S (ESOL) < 0 ☑ INSATU(Insaturation): 0.25 < Fraction Csp3 < 1 ☑ FLEX(Flexibility): 0 < Num. rotatable bonds < 9 If 6 descriptors of a natural plant ingredient satisfy the above rules, it will be labeled high HOB with the label of 1. Otherwise, a 0 will be assigned to the ingredient. Prediction_HobPre&SwissADME: If the ingredient was predicted to be high human oral bioavailability by both HobPre and SwissADME, the value will be 1. ========================================================================================= ====="CMAUPv2.0_download_Plant_molecular_targets_overlapping_with_DEGs": Disease_ID: the ID of 74 diseases analyzed for transcriptomic profiles. Plant_ID: Plant ID in CMAUP database Gene_Symbol/Plant_molecular_target: differentially expressed genes overlapping with molecular targets of individual plants. log2_fold_change: log2 transformed fold change (produced by DESeq2) adjusted_pval: adjusted p-value (produced by DESeq2) up_or_down_regulated_gene: up-regulated gene or down-regulated gene referring to the log2 fold-change. ========================================================================================= ====="CMAUPv2.0_download_Transcriptomic_profiling_of_74_diseases": There are one file and two folders included in this RAR file. 001_index_of_each_disease_analyzed_in_transcriptomic_change.txt: indexes of 74 analyzed diseases. 002_meta_data: sample information including data source and group (disease or control) of each disease. 003_Results_produced_by_DESeq2: dataframes produced by DESeq2. ========================================================================================= ====="CMAUPv2.0_download_Plant_Clinical_Trials_Associations": Plant_ID: Plant ID in CMAUP database NCT_ID: ClinicalTrials.gov registry number Title: title of the clinical trial Disease/Condition: the disease, disorder, syndrome, illness, or injury Form_in_Clinical_Use: name and ingredient ID of ingredients or name of individual plants Phase: trial phases displayed on ClinicalTrials.gov Associated_by_plant_or_ingredient: type of form in inclinical use (plant or ingredient) ========================================================================================= ====="CMAUPv2.0_download_Plant_Human_Disease_Associations": Plant_ID: Plant_ID ICD-11 Code: ICD-11 code number of the disease Disease_Category: category of the disease in ICD-11 Disease: formated disease name using ICD-11 coding tool Association_by_Therapeutic_Target: associated plant molecular targets Association_by_Disease_Transcriptiome_Reversion: associated differentially expressed genes overlapping with molecular targets of plant Association_by_Clinical_Trials_of_Plant: associated clinical investigations of plant Association_by_Clinical_Trials_of_Plant_Ingredients: associated clincial investigations of plant ingredient