Closed rbuels closed 5 years ago
I'm trying to munge some of the ensembl variation biomart because it has all the cosmic info, and then it just needs to join up to the actual cosmic vcf which has some sample info e.g. frequency of being mutated
Example of some ensembl biomart variation data
Variant name Variant source Chromosome/scaffold name Chromosome/scaffold position start (bp) Chromosome/scaffold position end (bp) Clinical significance Variant start in cDNA (bp) Variant end in cDNA (bp) Variant start in translation (aa) Variant end in translation (aa) Variant start in CDS (bp) Variant end in CDS (bp) Variant consequence Gene stable ID Transcript stable ID PolyPhen prediction PolyPhen score SIFT prediction SIFT score Variant Set Name P value Associated gene with phenotype Synonym name Synonym source Title Authors Year PubMed ID Variant Set Description Associated variant risk allele Associated variant names Source name Study external reference Study description Variant alleles 1000 Genomes global minor allele frequency (all individuals) 1000 Genomes global minor allele count (all individuals) Minor allele (ALL) Protein allele Consequence specific allele Biotype Transcript strand Distance to transcript Strand Phenotype description
COSM5956651 COSMIC 22 15528165 15528165 7 7 3 3 7 7 coding_sequence_variant ENSG00000130538 ENST00000252835 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION C/COSMIC_MUTATION protein_coding 1 6 1 Haematopoietic and lymphoid tissue tumour
COSM5956651 COSMIC 22 15528165 15528165 7 7 3 3 7 7 coding_sequence_variant ENSG00000130538 ENST00000252835 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION C/COSMIC_MUTATION protein_coding 1 6 1 Haematopoietic and lymphoid tissue tumour
COSM3842126 COSMIC 22 15528194 15528194 3 3 1 1 3 3 start_retained_variant ENSG00000130538 ENST00000643195 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION G/COSMIC_MUTATION protein_coding 1 2 1 Breast tumour
COSM3842126 COSMIC 22 15528194 15528194 36 36 12 12 36 36 coding_sequence_variant ENSG00000130538 ENST00000252835 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION G/COSMIC_MUTATION protein_coding 1 35 1 Breast tumour
COSM3842126 COSMIC 22 15528194 15528194 3 3 1 1 3 3 start_retained_variant ENSG00000130538 ENST00000643195 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION G/COSMIC_MUTATION protein_coding 1 2 1 Breast tumour
COSM3842126 COSMIC 22 15528194 15528194 36 36 12 12 36 36 coding_sequence_variant ENSG00000130538 ENST00000252835 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION G/COSMIC_MUTATION protein_coding 1 35 1 Breast tumour
COSM5834074 COSMIC 22 15528194 15528195 3 4 1 2 3 4 start_retained_variant ENSG00000130538 ENST00000643195 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION GA/COSMIC_MUTATION protein_coding 1 2 1 Breast tumour
COSM5834074 COSMIC 22 15528194 15528195 36 37 12 13 36 37 coding_sequence_variant ENSG00000130538 ENST00000252835 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION GA/COSMIC_MUTATION protein_coding 1 35 1 Breast tumour
COSM5834074 COSMIC 22 15528194 15528195 3 4 1 2 3 4 start_retained_variant ENSG00000130538 ENST00000643195 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION GA/COSMIC_MUTATION protein_coding 1 2 1 Breast tumour
COSM5834074 COSMIC 22 15528194 15528195 36 37 12 13 36 37 coding_sequence_variant ENSG00000130538 ENST00000252835 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION GA/COSMIC_MUTATION protein_coding 1 35 1 Breast tumour
COSM6883968 COSMIC 22 15528213 15528213 22 22 8 8 22 22 coding_sequence_variant ENSG00000130538 ENST00000643195 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION T/COSMIC_MUTATION protein_coding 1 21 1 Skin tumour
COSM6883968 COSMIC 22 15528213 15528213 55 55 19 19 55 55 coding_sequence_variant ENSG00000130538 ENST00000252835 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION T/COSMIC_MUTATION protein_coding 1 54 1 Skin tumour
COSM6883968 COSMIC 22 15528213 15528213 22 22 8 8 22 22 coding_sequence_variant ENSG00000130538 ENST00000643195 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION T/COSMIC_MUTATION protein_coding 1 21 1 Skin tumour
COSM6883968 COSMIC 22 15528213 15528213 55 55 19 19 55 55 coding_sequence_variant ENSG00000130538 ENST00000252835 COSMIC phenotype variants Phenotype annotations of somatic mutations found in human cancers from the COSMIC project COSMIC COSMIC_MUTATION T/COSMIC_MUTATION protein_coding 1 54 1 Skin tumour
COSM181480 COSMIC 22 15528254 15528254 63 63 21 21 63 63 coding_sequence_variant ENSG00000130538 ENST00000643195 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION C/COSMIC_MUTATION protein_coding 1 62 1 Endometrium tumour
COSM181480 COSMIC 22 15528254 15528254 96 96 32 32 96 96 coding_sequence_variant ENSG00000130538 ENST00000252835 All phenotype/disease-associated variants Variants that have been associated with a phenotype or a disease COSMIC COSMIC_MUTATION C/COSMIC_MUTATION protein_coding 1 95 1 Endometrium tumour
I have here variants and domains downloaded for a given protein https://github.com/cmdcolin/protein_data_service
I was thinking that I can make it also return sequence
If there is any other feedback on how data should be formatted let me know
One improvement could also include "collating multiple rows of the output" into a nested json structure
I think this is working, if there is a bug maybe we can open it in https://github.com/cmdcolin/protein_data_service
Little express.js-based web service that we will use to demo the protein viewer, that just takes a single human protein name as input (e.g. KRAS), picks the canonical isoform (if there are isoforms), and returns: