Deposit Your Datasets in DV-IMPACT

The main purpose of DV-IMPACT is to serve as a central resource for large-scale disease variant impact assessment studies and to make these data available online in a uniform format that guarantees data integration and interoperability between different datasets. This page lists the requirements for datasets deposition to DV-IMPACT . The dataset should comply with the DV-IMPACT standard data model (Table 1) and has the structure (or can be processed to be in the structure) that fits DV-IMPACT (Figure 1).

Data Items	Attributes	Type	Description
Mutations	Protein ID	Text	Standard protein identifier e.g. UniProt or Ensemble IDs (e.g. P04637 or ENSP00000269305).
	Mutation Type	Text	e.g. Substitution, Insertion, Deletion (as defined by mutation source database e.g. COSMIC).
	Mutation Description	Text	Should be in the standard form used by the major database and preceded by "p.". For instance, a substitution mutations will be "p.A1#A2", where A1 and A2 are the wildtype and the mutation amino acids, respectively, and # is the mutation position (e.g. p.P210R).
	Disease Name	Text	As mentioned in the original paper can also be abbreviated (e.g. AML for Acute Myeloid Leukemia).
	Mutation Source	Text	Database from where the mutations obtained (e.g. COSMIC, ICGC or TCGA).
	[O] Mutation ID	Text	The mutation identifier in the mutation source for reference.
	[O] Genomic Mutation Description	Text	Should be in the standard form used by the major database and preceded by "g." for genomic DNA. For instance, a substitution mutations in the DNA will be "g.N1#N2", where N1 and N2 are the wildtype and the mutation nucleotides, respectively, and # is the mutation position (e.g. g.A550C).
	[O] Mutation Recurrence	Number	How many times that same mutation was observed in the sample cohort it was identified in.
	[O] Mutation Samples	Number	Number of samples with the mutations to the total tested sample X/Y.
Domains	Domain ID	Text	Unique identifier for each domain instance.
	Domain InterPro ID	Text	The domain type identifier from InterPro Database.
	Protein ID	Text	Standard protein identifier of the protein where this domain is found.
	Domain Type	Text	The domain type as in from InterPro (e.g. SH2, SH3, WW, PDZ, Tyrosine-protein kinases).
	Domain Name	Text	A human readable name to identify the domain (e.g. ProteinName_# where ProteinName is the name of the protein where this domain is found and # is the order of the domains, in case of multiple domain proteins).
	Domain Coordinates*	Number	The domain start and end positions in the protein.
	[O] Other Proteins IDs	Text	Other proteins that have the same exact domain sequence.
Proteins	Protein ID	Text	Standard protein identifier e.g. UniProt or Ensemble IDs (e.g. P04637 or ENSP00000269305).
	Protein sequences	Text	The full protein sequence or the database and version information so that others can get the exact sequences was used in the predictions.
	[O] Protein Name	Text	Protein full name (e.g. Heat shock protein 90 for HSP90).
	[O] Gene Symbol	Text	Standard gene symbol (e.g. HGNC gene symbol).
	[O] Protein Description	Text	Additional information about the protein (e.g. other names, function or subcellular localization).
Interactions	Domain Protein ID	Text	The protein identifier of the protein of the domain as in the Domains data item.
	Peptide Protein ID	Text	The protein identifier of the protein of the peptide as in the Proteins data item.
	Domain ID	Text	The domain instance identifier as in the Domains data item.
	Wildtype Score	Number	Score/evaluation of wildtype predicted interaction e.g. p-value.
	Variant Score	Number	Score/evaluation of variant predicted interaction e.g. p-value.
	Binding Start*	Number	Peptide's start position.**
	Binding End*	Number	Peptide's end position.
	[O] Supporting Information	Text	Any information used to support the predicted PPI or rewiring event e.g. gene/protein expression, subcellular localization, disorder, surface accessibility or sequence conservation.
[O]PWMs	PWM Name	Text	A name to identify the PWM e.g. DomainName_# where DomainName is the name of the domain which this PWM corresponds to and # is the order of the PWM, in case of multiple specificity domains.
	PWM File	Text	Contains peptide sequences used to generate the PWM (in FASTA format) or the PWMs data.
	Domain ID	Text	The domain instance identifier as in the Domains data item.
	[O] Properties	Number	Any additional properties for the PWM e.g. score cut off or p-values.

[O] Optional data item or attribute.
* Alternately, the peptide sequence can be provided.
** all sequence coordinates start from 1.

Table 1. The data items and their required and optional attributes according to DV-IMPACT data standard.

Figure 1. Relationships between data items of DV-IMPACT standard data model for disease variants impact assessment. The relationships between the attributes correspond to the relationships between the tables in DV-IMPACT .

If you want to deposit your data into DV-IMPACT , please contact us.