CRISPR Screen Metadata
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Manually Curated Fields
Many of the manually curated fields in ORCS use controlled vocabularies developed by curators after a survey of the literature. These vocabularies are provided below.
| Field Name | Description |
|---|---|
| Screen Name | Each screen is assigned a number followed by the PubMed ID (e.g. 1-PMID26627737) to ensure publications with mulitple screens have a unique identfier for each individual screen. |
| Organism | Controlled vocabulary. |
| Screen Type | Controlled vocabulary based on survey of the data. Can be easily modified to accomodate new screen types that may be developed. |
| Experimental Setup | Controlled vocabulary based on survey of the data. Can be easily modified to accomodate new screen types that may be developed. |
| Duration | Controlled vocabulary of hours, days or doublings. |
| Condition Name/Condition Dosage | If the condition is a drug then add an Ontology ID from ChEBi, if a protein ligand add a UniProt ID. If a toxin or another term with no ID the ID field can be left blank. For the dosage there is a numeric field with an associated controlled vocabulary for units. A list of onotology terms currently in use in ORCS can be found here. |
| MOI | Optional (Multiplicity of Infection) should be entered if provided in the publication. |
| CRISPR Library Name/Type | Controlled vocabulary terms generated by survey of the literature. Can easily be modified as new libraries are developed. Accession IDs associated when possible. |
| Screen Format | Controlled vocabulary terms generated by survey of the literature. Can easily be modified as new screen formats are developed. |
| Enzyme | Controlled vocabulary terms generated by survey of the literature. Can easily be modified as new enzymes such as Base Editors are developed. |
| Cell Line/Type | Ontology terms from BTO (first choice), EFO (second choice) or CLO (third choice).Additional guidelines for this curation can be found here. |
| Phenotype | Ontology terms from APO, CMPO or Controlled Vocabulary as needed. Terms currently in use in ORCS can be found here. |
| Analysis Method | Controlled vocabulary terms generated by survey of the literature. Can easily be modified as new analysis methods are developed. |
| Significance Threshold | If provided by the authors a numeric significance threshold can be applied to any score column entered for a screen. Alternatively if only a list of hits was published the curator can mark the screen data as “all significant” or if a yes/no hit vaue was used the author can specify a boolean column. |