CRISPR Screen Metadata

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.

Back to ORCS Curation Guide

 
orcs/curation_guide/metadata_terms.txt · Last modified: 2020/06/02 15:20 by rose