slib.sglib.io.loader.bio.gaf2
Class EvidenceCodeRules

java.lang.Object
  extended by slib.sglib.io.loader.bio.gaf2.EvidenceCodeRules

public class EvidenceCodeRules
extends Object

Evidence codes are not statements of the quality of the annotation. Within each evidence code classification, some methods produce annotations of higher confidence or greater specificity than other methods, in addition the way in which a technique has been applied or interpreted in a paper will also affect the quality of the resulting annotation. Thus evidence codes cannot be used as a measure of the quality of the annotation. The EXP code is the parent code for the IDA, IPI, IMP, IGI and IEP experimental codes. Experimental Evidence Codes EXP: Inferred from Experiment -- IDA: Inferred from Direct Assay -- IPI: Inferred from Physical Interaction -- IMP: Inferred from Mutant Phenotype -- IGI: Inferred from Genetic Interaction -- IEP: Inferred from Expression Pattern Computational Analysis Evidence Codes ISS: Inferred from Sequence or Structural Similarity -- ISO: Inferred from Sequence Orthology -- ISA: Inferred from Sequence Alignment -- ISM: Inferred from Sequence Model IGC: Inferred from Genomic Context IBA: Inferred from Biological aspect of Ancestor IBD: Inferred from Biological aspect of Descendant IKR: Inferred from Key Residues IRD: Inferred from Rapid Divergence RCA: inferred from Reviewed Computational Analysis IEA: Inferred from Electronic Annotation Author Statement Evidence Codes TAS: Traceable Author Statement NAS: Non-traceable Author Statement Curator Statement Evidence Codes IC: Inferred by Curator ND: No biological Data available


Field Summary
static Set<String> EXPchildren
           
static Set<String> ISSchildren
           
 
Constructor Summary
EvidenceCodeRules()
           
 
Method Summary
static boolean areValid(Collection<String> ecCodesRestriction, String ec)
          Evaluate if a particular EC respect restrictions contains in a Collection of String defining invalid EC EC hierarchy is considered during the evaluation
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

EXPchildren

public static final Set<String> EXPchildren

ISSchildren

public static final Set<String> ISSchildren
Constructor Detail

EvidenceCodeRules

public EvidenceCodeRules()
Method Detail

areValid

public static boolean areValid(Collection<String> ecCodesRestriction,
                               String ec)
Evaluate if a particular EC respect restrictions contains in a Collection of String defining invalid EC EC hierarchy is considered during the evaluation

Parameters:
ecCodesRestriction - a Collection of String defining EC restrictions
ec - the EC evaluated
Returns:
boolean true if the evaluated EC is valid considered given restrictions


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