※ Data statistics for dbPTH
| Content | dbPTH 1.0 | BATMAN-TCM 2.0 | HIT 2.0 | HERB | TCMSP |
|---|---|---|---|---|---|
| Experimental Ingredient-target interactions (ITIs) | 165,967 | 17,068 | 10,031 | 4,815 | 3,970 |
| ITIs in total | 36,760,416 | 2,336,340 | 10,031 | N/A | N/A |
| Protein targets in total | 2,685,317 | 9,927 | 2,208 | 1,205 | 3,339 |
| Species | 1,139 | 2 | 4 | 2 | 1 |
| Ingredients in total | 4,856 | 39,171 | 1,237 | 49,258 | 29,384 |
| Data size | ~21.4 GB | ~79.3 MB | N/A | ~23.7 MB | N/A |
| Integrated information | Basic information, protein sequence, genetic variation & mutation, disease-associated information, protein-protein interaction, protein functional annotation, post-translational modification, target-herb relation, protein structural annotation, subcellular localization, biological pathway, protein expression/proteomics, domain annotation, physicochemical property, mRNA expression, and DNA & RNA element | Basic information, formula information | Basic information, strucuture information, herb inforamtion, protein functions | Basic information, disease information, herb inforamtion | Basic information, compound information, disease information, herb inforamtion |
※ Usage
In dbPTH, we tried to make it powerful and convenient to be used. The online service and local packages were provided. This USAGE is prepared for the online service. For usage of local packages, please download the Manual. The dbPTH 1.0 provide the search option and advance options.
1. Search. Four search options are provided, including simple search, advanced search, batch search and blast search for varies searching commands.
Note: dbPTH can display up to 10,000 results. For more results, we suggest adjusting your search by using more specific keywords to retrieve fewer results or by using only BLAST target protein in the case of BLAST search.
(1) Simple Search could be used to input one or multiple keywords (separated by space character) to search the dbPTH. The search fields including "PTH ID", "UniProt", "Protein Name", "Gene Name", "Ingredient", "PubChem" and "Species".
Example: You can click on the "Example" button to search "TRPV1" in "Gene Name" field. By clicking on the "Search" button, the related proteins will be shown.
(2) Advanced Search could be used to input two or more terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:
AND: The term following this operator has to be included in the specified field(s).
OR: Either the preceding or the following term to this operator should occur in the specified field(s).
NOT: If selected, the term following this operator must be not contained in the specified field(s).
Example: You can click on the "Example" button to load an instance, which could search protein "TRPV1" in "Homo sapiens". The human TRPV1 will be shown by clicking on the "Search" button.
(3) Batch Search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt accessions to search the database. The list should be inputed as one keyword one line.
Example: You can click on the "Example" button to load nine proteins UniProt accessions including "Q8NEB9", "Q8NEE8", "Q8NEG5", "Q8NEJ0", "Q8NEM0", "Q8NEM8", "Q8NER1", "Q8NES3", "Q8NEZ4" and "Q8NF91". By clicking on the "Search" button, you can find "TRPV1" and other proteins.
(4) BLAST Search could be used to find the specific protein and/or related homologues by sequence alignment. This search option will help you to find the querying protein quickly and accurately. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined. The default parameter of E-value is 0.00001.
Example: You can click on the "Example" button to load the protein sequence of "TRPV1" in "Homo sapiens". By clicking on the "Search" button, you can find the related homologues.
2. Browse. Three simple ways have been provided for users to browse proteins and ingredients in the database. Users can browse by protein subgroups or species for proteins and by chemical subtypes for ingredients.
(1) Browse by protein subgroups: You can select one of these protein subgroups to browse all proteins of corresponding subgroup.
(2) Browse by species: You can select one of these species to browse all proteins of corresponding species.
(3) Browse by chemical subtypes: You can select one of these chemical subtypes to browse all target-related ingredients of corresponding subtype.