Library File Formats
The file formats for library data follow the same guidelines as for any other resource of the Screensaver API. These guidelines are explained in data interchange.
Small Molecule Library
Data may be loaded using XLSX, CSV, or SDF format.
Chemical structure information (molfile) requires the SDF Format
Key fields
All library data uploads must define either a plate_number and well_name or alternatively, a well_id. ** The plate_number corresponds to a plate of the library, ** The well_id is the combination of the plate_number and the well_name.
General fields for upload
| Data Field | Is Required? | Format | Multi |
|---|---|---|---|
| plate_number | yes | positive integer | no |
| well_name | yes | letter A-P, followed by a number 1-24 (assumes 384-well plates) | no |
| well_id | yes | required if plate_number and well_name are not provided | no |
| well_type | yes | one of [“experimental”,”empty”,”dmso”] | no |
| vendor | yes | text | no |
| vendor_reagent_id | yes | text | no |
| vendor_batch_id | no | text | no |
| facility_id | no | text | no |
| molar_concentration | yes, if experimental well, optional otherwise. see format below. | concentration | |
| mg_ml_concentration | yes, if experimental well, optional otherwise. see format below. | concentration | |
| is_deprecated | no | boolean | no |
| deprecation_reason | no | text | no |
Small molecule fields for upload
| Data Field | Is Required? | Format | Multi |
|---|---|---|---|
| smiles | no | text | no |
| InChi | no | text | no |
| molecular_formula | no | text | no |
| molecular_mass | no | real number, up to 9 decimal places, 15 digits total | no |
| molecular_weight | no | real number, up to 9 decimal places, 15 digits total | no |
| compound_name | no | text | yes |
| pubmed_id | no | positive integer | yes |
| pubchem_cid | no | positive integer | yes |
| chembank_id | no | positive integer | yes |
| chembl_id | no | positive integer | yes |
Functional genomics fields for upload
| Data Field | Is Required? | Format | Multi |
|---|---|---|---|
| silencing_reagent_type | yes | text | yes |
| sequence | yes | text | no |
| anti_sense_sequence | yes | text | no |
| vendor_gene_name | yes | text | no |
| vendor_entrezgene_id | yes | integer | no |
| vendor_entrezgene_symbols | yes | text | yes |
| vendor_genebank_accession_numbers | yes | text | yes |
| vendor_species_name | yes | text | no |
| facility_gene_name | no | text | no |
| facility_entrezgene_id | no | integer | no |
| facility_entrezgene_symbols | no | text | yes |
| facility_genebank_accession_numbers | no | text | yes |
| facility_species_name | no | text | no |
| is_pool | no | boolean | no |
| duplex_wells | no | text | yes |
| is_restricted_sequence | no | boolean | yes |
Concentration values may be formatted as:
- ###.### mM
- ###.### uM
- ###.### nM
- ###.### pM
- ###.### mg/ml