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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ui

Figure 1: User Information.(1) name and email required for submisions.

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

  • Sort Acending/Decending

  • contains/does not contain'

  • empty/no empty'

  • null/notnull'

  • starts/ends/equal wtih'

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filter

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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bioactivities

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

  • Click on the “Download Template” clink and down the excel file template.

  • Fill the columns with required annotated data

  • Click 'Send for Review'

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bulk Import

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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Preview

Figure 6: Bulk import .(1) Edited fields are coloured green (2) Filter options

Add Annotations directly from search results

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Preview

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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Preview

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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submissions

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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Feedback