cleanMITAB.RdcleanMITAB extracts columns of molecular interaction data in MITAB 2.5 or 2.7 formats. For simple MITAB 2.5, columns are interactor Uniprot IDs(or other ID as specified by interactor_IDs_databases), interactor taxonomy IDs, Publication Identifiers, Confidence values and generates unique pair ID. MITAB 2.7 includes additional information: see details.
cleanMITAB(MITABdata)
| MITABdata | object of class "RAW_MItab25" or "RAW_MItab27" (list) containing molecular interaction data as returned by |
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Object of S3 class "clean_MItab25" or "clean_MItab27" containing interaction data in a data.table. Within each interacting pair all interactor attributes are sorted according to alphanumerically sorted interactor UniprotKB accessions
Output column description (MITAB 2.5):
pair_id - unique identifier of the undirected interaction: ordered alphabetically and concatenated interacting molecule IDs
IDs_interactor_A, IDs_interactor_B - interacting molecule ID
interactor_IDs_databases_A, interactor_IDs_databases_B - database that provides interacting molecule ID such as UniProt, ChEMBL or IntAct (IntAct: when the molecule cannot be mapped to ID in any other resource)
Taxid_interactor_A, Taxid_interactor_B - taxonomic species that interacting molecule belongs to
Publication_Identifiers - pubmed ID of the papers that has reported the interaction
Confidence_values - MIscore. Details: https://psicquic.github.io/MITAB25Format.html, http://www.ebi.ac.uk/intact/pages/faq/faq.xhtml, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316181/
if MITAB 2.7 then the following columns are added:
Host_organisms - taxid of organism in which the interaction detections experiment was performed
bait_prey_status_A, bait_prey_status_B - specifies the experimental role of a protein: a bait, a prey, a neutral component or else (http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:0495)
Interaction_detection_methods - Method to determine the interaction. http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:0001
Interaction_types - http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:0190
Interaction_identifiers - Interaction identifier given by database (e.g. intact:EBI-1547321|imex:IM-11865-3)
Expansion_methods - The method by which complex n-ary data is expanded into binary data. http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:1059
Features_interactor_A, Features_interactor_B - Property of a subsequence that may interfere with the binding of a molecule. http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:0116
Identification_method_participant_A, Identification_method_participant_B - Method to determine the molecules involved in the interaction. http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:0002
binding_region_A_start, binding_region_A_end, binding_region_B_start, binding_region_B_end - start and end position of binding-associated features
binding_region_A_type, binding_region_B_type - Type of the binding region. Details: http://www.ebi.ac.uk/ols/ontologies/MI/terms?obo_id=MI:0117, https://psicquic.github.io/MITAB27Format.html, MITABregionFeature