Data table formats

MaveDB accepts and provides data tables in CSV format. Each row of the data table describes a single variant, and variants are described using MAVE-HGVS format. All other columns are expected to be floating point values.

Variant columns

For both score and count data tables, there are three variant columns:

• hgvs_nt describes variants with respect to the nucleotide target sequence

• hgvs_tx describes variants with respect to a transcript model

• hgvs_pro describes variants with respect to the amino acid target sequence

hgvs_nt and hgvs_pro variants are required to be described in relation to the score set target sequence, rather than to an external reference sequence.

If hgvs_nt is present, it will be used as the primary key for distinguishing variants and must be unique. Otherwise, hgvs_pro will be used as the primary key.

Note

Datasets with only hgvs_pro variants can specify nucleotide target sequences. The target sequence will be translated using the standard amino acid translation table for validation.

The hgvs_tx variants are not validated against a transcript model or target sequence. This is a convenience feature for datasets that contain splice variants; most datasets will not use hgvs_tx. Datasets that use hgvs_tx must also have hgvs_nt, which is used as the primary key, and the hgvs_nt variants must use the 'g.' prefix.

Score table columns

All score tables must have a column named score that describes the score of that variant in the assay. Score tables may have any number of additional numeric columns.

Suggested numeric columns include a standard deviation or variance, or some other measure of uncertainty for the score such as a 95% confidence interval (represented as two columns, e.g. ci_lower and ci_upper).

Score sets that describe experiments with multiple replicates often include the score and standard deviation for each replicate as additional columns.

For datasets with categorical data, we recommend encoding the categories as integers and describing the mapping between integers and categories in the free text methods. Support for additional data columns with string data will be added in a future version to support this use case.

Score table examples

Here is a short excerpt from the score table for urn:mavedb:00000003-a-1.

That this dataset uses hgvs_nt as the primary variant key. It has several additional data columns with the scores and error estimates for multiple biological replicates.

Note that some variants do not have a score. This is permitted (and encouraged) as long as there is some data provided for that variant, such as a score in an individual replicate or some counts.

Table 1 Example Score Data

hgvs_nt	hgvs_splice	hgvs_pro	score	SE	epsilon	SE_PlusE2NewRep3	score_PlusE2NewRep3	SE_PlusE2NewRep4	score_PlusE2NewRep4	SE_PlusE2NewRep5	score_PlusE2NewRep5	SE_PlusE2Rep3	score_PlusE2Rep3	SE_PlusE2Rep4	score_PlusE2Rep4	SE_PlusE2Rep5	score_PlusE2Rep5
c.38T>C	NA	p.Val13Ala	-0.128	0.115	0.000	0.148	0.283	0.162	-0.456	0.075	-0.186	0.167	-0.165	0.289	-0.073	0.388	-0.184
c.186A>T	NA	p.Leu62Phe	-4.132	0.396	0.000	0.289	-3.752	0.433	-4.166	0.549	-3.456	0.341	-3.166	0.499	-6.079	0.204	-4.309
c.164A>T	NA	p.Lys55Ile	-0.655	0.112	0.000	0.100	-0.592	0.121	-0.929	0.086	-0.254	0.143	-0.695	0.039	-0.950	0.080	-0.514
c.[439C>A;441G>A;842C>A]	NA	p.[Gln147Lys;Ser281Ter]	NA	NA	NA	0.668	-1.612	NA	NA	NA	NA	NA	NA	NA	NA	0.464	-1.273
c.22_23delinsCC]	NA	p.Glu8Pro	-0.375	0.280	0.000	0.158	-1.421	0.240	-0.265	0.200	-0.796	0.192	-0.022	0.311	-0.232	0.091	0.476
c.598G>A	NA	p.Asp200Asn	0.271	0.170	0.000	0.103	-0.337	0.094	0.830	0.092	0.408	0.163	0.051	0.243	0.278	0.172	0.382
c.285C>G	NA	p.Asp95Glu	NA	NA	NA	0.401	-3.993	0.150	-3.380	NA	NA	0.452	-3.221	0.228	-1.973	0.277	-1.774
c.[64G>C;142C>T]	NA	p.Glu22Gln	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
c.869T>G	NA	p.Leu290Ter	-1.231	0.245	0.000	0.117	-0.456	0.285	-0.792	0.424	-0.993	0.084	-1.909	0.143	-1.325	0.093	-1.735
c.200T>G	NA	p.Ile67Arg	NA	NA	NA	0.255	-3.600	0.152	-3.399	NA	NA	0.171	-4.097	0.361	-3.764	NA	NA
c.[1G>T;97_99delinsGGG]	NA	p.[Asp1Tyr;Pro33Gly]	NA	NA	NA	0.159	-0.177	0.445	-0.583	0.500	-0.323	0.537	-0.470	NA	NA	0.284	0.188
c.476G>T	NA	p.Gly159Val	-1.192	0.100	0.000	0.141	-1.050	0.079	-1.557	0.030	-0.969	0.114	-1.030	0.126	-1.264	0.168	-1.303

Count table columns

Count data are optional for MaveDB score sets, but are recommended.

There are no required columns for count data, but uploaders should decide on an intuitive naming convention for the column names and describe it in the free text methods.