Mapping of terms to MI term ids - iRefIndex 6.0

In those cases where an interaction data record lists a term where a controlled vocabulary term is expected, and no controlled vocabulary term identifier is found, the term found in the record will be mapped by a curator to the closest possible term identifier using the molecular interaction ontology.

These corrections are made in two cases.

1) For interaction types where no cv term id is listed.

2) For interaction detection types where no cv term id is listed.

The mappings used are shown below. Feedback (and corrections) by databases is welcome. ian.donaldson@biotek.uio.no

These mappings are reviewed from one release to another.

Additional details are available at http://www.ebi.ac.uk/ontology-lookup/

Interaction Type Terms

term found in record	curator-assigned term id	assigned term	notes
Co-fractionation	MI:0403	colocalization	Interaction detection method name used inappropriately as a interaction type name
Affinity Capture-Western	MI:0914	association	Interaction detection method name used inappropriately as a interaction type name
Dosage Rescue	MI:0796	suppressive genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - assuming that the rescuing background had WT phenotype
Synthetic Rescue	MI:0796	suppressive genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - assuming that the rescuing background had WT phenotype
Synthetic Lethality	MI:0794	synthetic genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - assuming that the a and b background had WT phenotype
Synthetic Growth Defect	MI:0794	synthetic genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - assuming that the a and b background had WT phenotype
Dosage Lethality	MI:0794	synthetic genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - assuming that the a and b background had WT phenotype
Phenotypic Enhancement	MI:0799	synthetic genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - assuming that enhancing b background had WT phenotype
Phenotypic Suppression	MI:0796	suppressive genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - here it is difficult to say what the inequality between a, b, ab and WT is.
Dosage Growth Defect	MI:0931	genetic interaction defined by inequality	Interaction detection method name used inappropriately as a interaction type name - here i am assuming that the rescuing b background had WT phenotype
Affinity Capture-MS	MI:0914	association	Interaction detection method name used inappropriately as a interaction type name
Co-crystal Structure	MI:0915	physical association	Interaction detection method name used inappropriately as a interaction type name
Co-purification	MI:0914	association	Interaction detection method name used inappropriately as a interaction type name
Affinity Capture-Luminescence	MI:0914	association	Interaction detection method name used inappropriately as a interaction type name
Affinity Capture-RNA	MI:0914	association	Interaction detection method name used inappropriately as a interaction type name
Synthetic Haploinsufficiency	MI:0208	genetic interaction	Interaction detection method name used inappropriately as a interaction type name
DNA replication elongation	MI:0190	interaction type?	Impossible to map. These examples should be looked at. Map to root term for interaction type.
FRET	MI:0914	association	Interaction detection method name used inappropriately as a interaction type name
PCA	MI:0915	physical association	99% of the time when 2 hybrid is the method, the database will list the interaction as MI:0915 (physical interaction)
Two-hybrid	MI:0915	physical association	99% of the time when 2 hybrid is the method, the database will list the interaction as MI:0915 (physical interaction)
Co-localization	MI:0403	colocalization	Interaction detection method name used inappropriately as a interaction type name
Reconstituted Complex	MI:0915	physical association
Biochemical Activity	MI:0915	physical association?	Individual examples should be reviewed
Protein-peptide	MI:0407	direct interaction
Protein-RNA	MI:0915	physical association
Biochemical reaction	MI:0915	physical association?	Individual examples should be reviewed
covalent interaction	MI:0195	direct interaction
Far Western	MI:0407	direct interaction	Depends how the experiment was done. Individual cases should be examined. Interaction detection method name used inappropriately as a interaction type name
phosphorylation reaction	MI:0217	phosphorylation reaction	Correct term. MI term id was simply missing
dna strand elongation	MI:0701	dna strand elongation	Correct term. MI term id was simply missing
methylation reaction	MI:0213	methylation reaction	Correct term. MI term id was simply missing
dephosphorylation reaction	MI:0203	dephosphorylation reaction	Correct term. MI term id was simply missing
demethylation reaction	MI:0871	demethylation reaction	Correct term. MI term id was simply missing
acetylation reaction	MI:0192	acetylation reaction	Correct term. MI term id was simply missing
ubiquitination reaction	MI:0220	ubiquitination reaction	Correct term. MI term id was simply missing
cleavage reaction	MI:0194	cleavage reaction	Correct term. MI term id was simply missing
deacetylation reaction	MI:0197	deacetylation reaction	Correct term. MI term id was simply missing
adp ribosylation reaction	MI:0557	adp ribosylation reaction	Correct term. MI term id was simply missing
sumoylation reaction	MI:0566	sumoylation reaction	Correct term. MI term id was simply missing
phosphotransfer reaction	MI:0844	phosphotransfer reaction	Correct term. MI term id was simply missing
neddylation reaction	MI:0567	neddylation reaction	Correct term. MI term id was simply missing
palmitoylation reaction	MI:0216	palmitoylation reaction	Correct term. MI term id was simply missing
deneddylation reaction	MI:0569	deneddylation reaction	Correct term. MI term id was simply missing
deubiquitination reaction	MI:0204	deubiquitination reaction	Correct term. MI term id was simply missing
glycosylation reaction	MI:0559	glycosylation reaction	Correct term. MI term id was simply missing
hydroxylation reaction	MI:0210	hydroxylation reaction	Correct term. MI term id was simply missing
amidation reaction	MI:0193	amidation reaction	Correct term. MI term id was simply missing

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