Introduction
Drug Target Commons (DTC) is a community based effort to improve the consensus on drug-target interactions. Our system contains two types of bioactivity data i.e. annotated and annotated. Initial search on 'Home page' allows the users to view existing (unannotated) bioactivity data using compound, target or publications. However, users may submit suggestions to edit/add bioactivity data and MicroBAO annotations.
User Information/login
DTC data has open access but user information(name and email)/login is required if the user is submitting annotations .This is to avoid spam.To login, user can use google account/Fimm user verification .
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Figure 1: User Information.(1) name and email required for submisions.
Search
Search keyword are matched with annotated/unannotated compounds, targets and publications, therefor you get a combined set of results from which you select the preferred result.
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Figure 2: Search Example: (1) Search bar,add text to search (2) Search Results table, list compounds,targets and mutations matching the search. (3) Bioactivities, list of bioactivites for the selected target,compound or mutation.
Compound search
Compound search can be by name or synonyms, standard inchikey or any of 26 IDs (Chembl, bindingdb, molport, surechembl, actor, nmrshiftdb2, chebi, hmdb, fdasrs, selleck, lincs, drugbank, nih_ncc, pharmgkb, ibm, nikkaji, pubchem, emolecules, zinc, recon, mcule, pubchem_dotf, gtopdb, pdb, pubchem_tpharma, kegg_ligand). Partial and exact searches are supportable for compound name or synonyms; while inchikey or IDs must have exact match. After entering compound name or ID, user must have to click on search button (or press enter key) to search it in present database.
Target search
Target search can be made by target name, gene name and ID (UniProtKB-AC, UniProtKB-ID, EMBL-CDS, Ensembl, PIR, PubMed, NCBI-taxon, Ensembl_TRS, MIM, UniGene, UniRef50, RefSeq, GO, PDB, UniParc, Additional PubMed, EMBL, GI, GeneID, Chembl, UniRef100, UniRef90, Ensembl_PRO) . Rest of specifications are more or less similar to compound search. Again same filter on target types. User may perform filtering, searcing, reordering of columns and export to excell to the resulting records.
Publication search
Publication search can be done using "Pubmed ID". If "pubmed ID" information doesn’t exists in our present database user may manually enter all the fields. If ‘pubmed ID’ information exists in our system, than some of the information about compound, targets, bioactivities, assays and publication will be retrieved automatically. However MicroBAO and few more fields will be left blank for user. Again, User may filter out irrelevant compounds or targets.
Filter
Following filters are avaialble
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Sort Acending/Decending
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contains/does not contain'
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empty/no empty'
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null/notnull'
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starts/ends/equal wtih'
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Figure 3: (1) Filter icon.(2) Sort options. (3) Other filter options.
Annotations
Bioactivites are either annotated( highlight in blue ) or unannotated and only unannotated bioactivites can be edited.
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Figure 4: Bioactivities.(1) Annotated (2) Unannotated.
Add annotations
Annotations can be added by uploading a excel file(suitable for large data) or directly from search results
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Click on the “Download Template” clink and down the excel file template.
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Fill the columns with required annotated data
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Click ' Send for Review '
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Figure 5: (A)Bulk import .(1) Download example template (2) Upload new Annoataions.
Uploaded Annotations can be previewed and edited before submitting
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Figure 6: Bulk import .(1) Edited fields are coloured green (2) Filter options
Add Annotations directly from search results
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Figure 7: Add Annotations .(1) You can export the data into and excel sheet and edit it (2) Disabled because no annotations has been edited.
edited fields will turn green after edit
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Figure 8: Add Annotations .(1) Edited fields are colored green. (2) Disabled because no annotations has been edited.(2) Once all changes are complete click ” Send for Review”, you will be asked user credentials if you are not logged in
Submission
All submitted annotations can be viewed in the submission page, which will be reviewed and approved or disapproved by the Admin.
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Feedback
a)Feedback form: Feedback button is available on the right side of all pages. Click to submit your suggestions or issues while using DTC.
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