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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