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orcs:curation_guide:metadata_terms [2019/06/27 09:20]
jenn
orcs:curation_guide:metadata_terms [2022/07/12 13:54] (current)
jenn
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-======= ​Manually Curated Fields ​=======+======= ​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. 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 ​      ^ ^  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. | +^  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 ​Type  ​| ​[[orcs:​controlled_vocabulary|Controlled vocabulary]] based on survey ​of the dataCan be easily modified ​to accomodate new screen types that may be developed. | +^  Screen ​Rationale ​ ​| ​A free text field to succinctly describe the purpose ​of the screen in order to provide additional context for the significance of hitsCommon 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 accomodate ​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 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 [[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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 ^  Cell Line/​Type ​ | Ontology terms from BTO (first choice), EFO (second choice) or CLO (third choice).Additional guidelines for this curation can be [[orcs:​cell_line_guidelines|found here]].| ^  Cell Line/​Type ​ | Ontology terms from BTO (first choice), EFO (second choice) or CLO (third choice).Additional guidelines for this curation can be [[orcs:​cell_line_guidelines|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]]. | ^  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_vocabulary5|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 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. |+^  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 methodIf 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.1561641636.txt.gz · Last modified: 2019/06/27 09:20 by jenn