In this database, the REST API uses HTTP queries to retrieve all meaningful biological information. Queries to most of the endpoints can be refined by adding filters, which are often shared among many endpoints - it makes the system easier to learn and use, as the same syntax is always valid across different endpoints. In case of any problems see troubleshooting section at the end of this document.
The output is in JSON format.
By default, you will get results for all mutations sets. For instructions to specify only one or subset of dataset, please refer to filters section.
An empty response (404 or '') or a verbose warning (see below) indicates that there are no mutations in the chosen dataset.
Get a single, point mutation.
Both known (already annotated and accessible in one of our datasets) and novel mutations are returned by this endpoint until a dataset filter is specified.
If there is no mutation matching the given filters, a warning: Warning: There is a mutation, but it does not satisfy given filters is returned.
|mutated_residue (alternative) amino acid||L|
A novel mutation in TP53, isoform NM_000546:
A known mutation in TP53 (it belongs to MC3/TCGA mutations dataset):
TP53 R282W is a known mutation in TP53. It belongs to three mutation datasets: MC3/TCGA, ClinVar and ESP6500.
all data about TP53 R282W:
try to get data for The 1000 Genomes Project:
In the last case, the server issues warning: such a mutation is possible but it does not match specified criteria.
It is because this mutation was not detected in The 1000 Genomes Project study.
All known mutations in given isoform sequence
Return all mutations from given isoform which belong to any of our datasets. Mutations returned by this endpoint are known that is they are in one of ours datasets.
Get all mutations in gene `NM_000123` and from dataset ESP6500:
Network representation is provided as "network" attribute of an object returned by endpoint with following attributes:
All genomic coordinates are 1-based. Stop codon and silent mutations are not considered.
Single DNA mutation
This endpoint allows you to convert genomic position to resultant protein mutation and retrieve all information about this mutation. If the mutation does not map to a known coding sequence, an empty response will be returned.
Please note that this endpoint is strand sensitive - if your gene of interest is placed on reverse strand (as defined in hg19/GRCh37) you need to provide nucleotides as on reverse strand (e.g. reference should be complementary to the forward strand).
You can specify one or more filters by appending 'filters' query string to any of endpoints. Remember to start from a question mark and add equality sign after word 'filters'. It should look like:
A single filter
You should specify three things for each filter:
1. A target (an accessor; which property from which model should be taken into account)
2. A comparator (how the value of given target should be compared to the value that you will specify)
3. A value (which values of target you want to include/exclude, use to compare)
The three elements are separated by colons, so a single filter should be like:
Combining filters means that both filters should be satisfied for given entity ("and" joining).
To combine filters, separate them with semicolons:
You can add more than one value (separated by commas) if it is sensible for given comparator. For example, you can write:
There is a number of comparators available. Often filters restrict the use of comparators to specified subset which is called "allowed comparators". It is often the case for values or targets that are list-based - then only operators like 'in' or 'ni' are sensible.
Following comparators might be used:
|ge||is x greater or equal to y?|
|le||is x lower or equal to y?|
|gt||is x greater than y?|
|lt||is x lower than y?|
|eq||is x equal to y?|
|in||does x contain y?|
|ni||does y contain x?|
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