slib.sglib.io.loader.bio.gaf2
Class EvidenceCodeRules
java.lang.Object
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
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 |
EXPchildren
public static final Set<String> EXPchildren
ISSchildren
public static final Set<String> ISSchildren
EvidenceCodeRules
public EvidenceCodeRules()
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 restrictionsec
- the EC evaluated
- Returns:
- boolean true if the evaluated EC is valid considered given restrictions
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