Upload Wizard: Difference between revisions
| (10 intermediate revisions by the same user not shown) | |||
| Line 7: | Line 7: | ||
== Version Releases == | == Version Releases == | ||
09-10-2019 : Beta v.0 | 09-10-2019 : Beta v.1.0 | ||
== Getting Started == | == Getting Started == | ||
| Line 25: | Line 25: | ||
* CSV/TSV format file | * CSV/TSV format file | ||
Fields are the column name of the catalog: | Fields are the column name of the catalog: | ||
Mandatory: Smiles, ID Field | |||
Optional: Price, Compound Name, CAS | |||
== Upload instructions == | == Upload instructions == | ||
=== Catalog File Splitting Instruction === | === Catalog File Splitting Instruction === | ||
[[File:upload.png| | [[File:upload.png|300px|right|alt upload page]] | ||
* Catalog Type: | * Catalog Type: | ||
We categorize compounds into 5 main groups: | |||
- Screening Compounds | |||
- Building Blocks | |||
- Natural Products | |||
- Bioactives | |||
- Mixed | |||
* Availability Type: | |||
In order to automate the current catalog update pipeline, '''each catalog ought to be specified when upload if it is a in-stock or on-demand'''. This information is important when we organize molecules on ZINC by [http://zinc.docking.org/tranches/home/ tranches] for Large-Scaled Docking. | In order to automate the current catalog update pipeline, '''each catalog ought to be specified when upload if it is a in-stock or on-demand'''. This information is important when we organize molecules on ZINC by [http://zinc.docking.org/tranches/home/ tranches] for Large-Scaled Docking. | ||
* Upload Type: | |||
Please specify if catalog is full update or incremental update for their upload procedure for updating catalog are different. | |||
=== File Format Supported === | === File Format Supported === | ||
| Line 46: | Line 57: | ||
* SMI/TXT - Text File format (with only smiles and product code, great for large catalog update) | * SMI/TXT - Text File format (with only smiles and product code, great for large catalog update) | ||
<div class="toccolours mw-collapsible mw-collapsed" style="overflow:auto;"> | <div class="toccolours mw-collapsible mw-collapsed" style="overflow:auto;"> | ||
<div style="font-weight:bold;line-height:1.6;">Special instruction for SMI/TXT catalog</div> | <div style="font-weight:bold;line-height:1.6;">READ ME: Special instruction for SMI/TXT catalog</div> | ||
<div class="mw-collapsible-content"> | <div class="mw-collapsible-content"> | ||
Files in SMI and TXT format must follow this format: | Files in SMI and TXT format must follow this format: | ||
| Line 73: | Line 84: | ||
[[ File:upload_wizard_pipeline.png | 700px ]] | [[ File:upload_wizard_pipeline.png | 700px ]] | ||
== Future Improment == | |||
* Automate the filtering procedure. | |||
== Admin Instruction == | |||
* Something here | |||
[[Category: ZINC]] [[Category:Website]] [[Category:Khanh]] | |||
Latest revision as of 18:01, 28 October 2019
Background
Upload Wizard is file-transfering website written by Chinzo and maintained by Khanh from Irwin Lab at UCSF. The aim for this website is to provide a easier way for ZINC vendors send catalogs updates on ZINC in oppose to sending us email in the past.
NOTE (09-6-2019): This is a beta release. Any suggestions and comments are greatly appreciated.
Version Releases
09-10-2019 : Beta v.1.0
Getting Started
Vendor must sign up to use Upload Wizard
Sign up
- Submit a form request to us by clicking on this link and choose "Sign Up" at the bottom. Please also tell us briefly about you and your company in 140 words or less.
- After you submitted your information, you will receive an email asking to confirm your email.
- Our admin will review your request and get back to you ASAP (Due to security reason, this step is important; it might take a bit of time, thank you for your patient).
Company Form
You are required to fill in Company Profile before uploading catalog
Instruction of filling in "Catalog Info" section:
- CSV/TSV format file
Fields are the column name of the catalog:
Mandatory: Smiles, ID Field Optional: Price, Compound Name, CAS
Upload instructions
Catalog File Splitting Instruction
- Catalog Type:
We categorize compounds into 5 main groups:
- Screening Compounds
- Building Blocks
- Natural Products
- Bioactives
- Mixed
- Availability Type:
In order to automate the current catalog update pipeline, each catalog ought to be specified when upload if it is a in-stock or on-demand. This information is important when we organize molecules on ZINC by tranches for Large-Scaled Docking.
- Upload Type:
Please specify if catalog is full update or incremental update for their upload procedure for updating catalog are different.
File Format Supported
Upload Wizard is current supporting catalog formats:
- SDF - Scientific Data File
- CSV/TSV - Delimiter Separated File
- SMI/TXT - Text File format (with only smiles and product code, great for large catalog update)
Excel file formats are not supported yet. In order to work around this, please Save file as Window Formatted TSV or CSV file
Limit File Size
Upload up to 1GB file per upload. That is approximately:
- ~18M smiles on a TXT/SMI file
- ~500k on an SDF file
Pipeline
Semi automatic scheme of Upload Wizard
Future Improment
- Automate the filtering procedure.
Admin Instruction
- Something here