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orcs:curation_guide:metadata_terms [2022/07/12 11:13]
jenn
orcs:curation_guide:metadata_terms [2022/07/12 13:54] (current)
jenn
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 ^  Field Name  ^ Description ​      ^ ^  Field Name  ^ Description ​      ^
 ^  Screen Name  |Each screen is assigned a number followed by the PubMed ID (e.g. 1-PMID26627737) to ensure publications with multiple screens have a unique identifier for each individual screen. | ^  Screen Name  |Each screen is assigned a number followed by the PubMed ID (e.g. 1-PMID26627737) to ensure publications with multiple screens have a unique identifier for each individual screen. |
-^  Organism ​ | Controlled vocabulary. | +^  Organism ​ | Controlled vocabulary ​[[orcs:​supported organisms|found here]]. | 
-^  Screen Rationale ​ | A free text field designed for curators ​to succinctly describe the purpose of the screen to provide additional context for the significance of hits. Common rationales include "Cell essential genes" or "​Increased drug resistance"​ but allow the freedom for added specificity when needed such as "Tumor response to drug treatment"​. |+^  Screen Rationale ​ | A free text field to succinctly describe the purpose of the screen ​in order to provide additional context for the significance of hits. Common rationales include "Cell essential genes" or "​Increased drug resistance"​ but allow the freedom for added specificity when needed such as "Tumor response to drug treatment"​. |
 ^  Experimental Setup  | [[orcs:​controlled_vocabulary2|Controlled vocabulary]] based on survey of the data. Can be easily modified to accommodate new screen types that may be developed. | ^  Experimental Setup  | [[orcs:​controlled_vocabulary2|Controlled vocabulary]] based on survey of the data. Can be easily modified to accommodate new screen types that may be developed. |
 ^  Duration ​ | Controlled vocabulary of hours, days or doublings. | ^  Duration ​ | Controlled vocabulary of hours, days or doublings. |
-^  Condition Name/​Condition Dosage ​ | If the condition is a drug then add an Ontology ​ID from ChEBiif a protein ligand ​add a UniProt ID, if a virus or bacteria ​add taxon ID, if a mutation ​add relevant gene ID. If a toxinrelevant culture condition ​or another term with no ID the ID field can be left blank. Currently if multiple conditions need to be specified for a screen (usually a mutation in addition to another condition) they can be separated using a pipe character. For the dosage there is a numeric field with an associated controlled vocabulary for units. A list of ontology terms currently in use in ORCS can be [[orcs:​conditional_onotology_terms|found here]]. |+^  Condition Name/​Condition Dosage ​ | Ontology IDs are added for various conditions: ​drug/chemical (ChEBI ​ID), protein ligand ​(UniProt ID), virus or bacteria ​(Taxon ​ID), mutation ​(relevant gene ID). If a condition does not have an applicable ID, such as a toxin or relevant culture condition the ID field is left blank. Currently if multiple conditions need to be specified for a screen (usually a mutation in addition to another condition) they can be separated using a pipe character. For the dosage there is a numeric field with an associated controlled vocabulary for units. A list of ontology terms currently in use in ORCS can be [[orcs:​conditional_onotology_terms|found here]]. |
 ^  MOI  | Optional (Multiplicity of Infection) should be entered if provided in the publication. | ^  MOI  | Optional (Multiplicity of Infection) should be entered if provided in the publication. |
 ^  CRISPR Library Name/​Type ​ | [[orcs:​controlled_vocabulary3|Controlled vocabulary]] terms generated by survey of the literature. Can easily be modified as new libraries are developed. Accession IDs associated when possible.| ^  CRISPR Library Name/​Type ​ | [[orcs:​controlled_vocabulary3|Controlled vocabulary]] terms generated by survey of the literature. Can easily be modified as new libraries are developed. Accession IDs associated when possible.|
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 ^  Phenotype ​ | Ontology terms from APO, CMPO or Controlled Vocabulary as needed. Terms currently in use in ORCS can be [[orcs:​phenotype_terms|found here]]. | ^  Phenotype ​ | Ontology terms from APO, CMPO or Controlled Vocabulary as needed. Terms currently in use in ORCS can be [[orcs:​phenotype_terms|found here]]. |
 ^  Analysis Method ​ | [[orcs:​controlled_vocabulary6|Controlled vocabulary]] terms generated by survey of the literature. Can easily be modified as new analysis methods are developed. | ^  Analysis Method ​ | [[orcs:​controlled_vocabulary6|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 ​numeric ​significance threshold can be applied to any score column ​entered ​for a screenand even to multiple score columns ​if necessary ​based on analysis method. ​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 value was used the author ​can specify ​a boolean column. |+^  Significance Threshold ​ |When a significance threshold ​is given in a paper, it can be applied to any score column for a screen and even to multiple score columns based on the analysis method. ​If only a list of significant ​hits was published, then all of the gene hits are uploaded ​as all significant”. Alternatively, ​if a yes/no hit value was used to identify gene hits in a paper, then the genes can be uploaded by specifying they'​re hit status using a boolean column. |
  
 [[:​orcs:​curation_guide|Back to ORCS Curation Guide]] [[:​orcs:​curation_guide|Back to ORCS Curation Guide]]
 
orcs/curation_guide/metadata_terms.txt · Last modified: 2022/07/12 13:54 by jenn