Update grch37 HGNC, Mutation Assessor and ClinVar #96
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leexgh
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leexgh
changed the title
| @@ -1,10 +1,10 @@ | |||
| name version type id description url | |||
| VEP grch37 mirrored vep VEP determines the effect of your variants(SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. https://grch37.ensembl.org/info/docs/tools/vep/index.html | |||
| HGNC 2023-10 mirrored hgnc The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/ | |||
| HGNC 2024-10 mirrored hgnc The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/ | |||
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@leexgh for the version formatting of hgnc, can you align with @rmadupuri so it's similar to the proposed cBioPortal version. I think this was proposed:
hgnc_v2023.10.1 similar to the genesets version in the [cBioPortal] database to indicate the HGNC release date of the data used to create the tables
Thanks!
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Check with Ramya, change to hgnc_v2024.10.1
| "https://genome-nexus-static-data.s3.us-east-1.amazonaws.com/mutationassessor_v4_1.tsv.gz" | ||
| "https://genome-nexus-static-data.s3.us-east-1.amazonaws.com/mutationassessor_v4_2.tsv.gz" | ||
| "https://genome-nexus-static-data.s3.us-east-1.amazonaws.com/mutationassessor_v4_3.tsv.gz" | ||
| "https://genome-nexus-static-data.s3.us-east-1.amazonaws.com/mutationassessor_v4_4.tsv.gz" |
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@leexgh is the process described somewhere for how these files are updated on S3?
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I'll have a follow-up PR to describe files on S3 and how to update them
| PDB latest external pdb A resource for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids. https://www.rcsb.org/ | ||
| xrefs latest external xrefs Xref endpoint is a lookup of Ensembl Identifiers and retrieve their external references in other databases http://grch37.rest.ensembl.org/ | ||
| PFAM 32.0 mirrored pfam A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. https://www.ebi.ac.uk/interpro/ | ||
| PTM dbPTM 2019 mirrored ptm A resource for protein post-translational modifications (PTMs). https://awi.cuhk.edu.cn/dbPTM/ |
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The PTM url we have in the MAKEFILE is down, this is their new website. They don't have a version number on the new or previous website, I add dbPTM 2019 as the version because this is the time we added PTM so I assume we were adding the latest at that time
| Polyphen-2 2.2.3, release 405c external polyphen "PolyPhen-2 predicts the effect of an amino acid substitution on the structure and function of a protein using sequence homology, Pfam annotations, 3D structures from PDB where available, and a number of other databases and tools (including DSSP, ncoils etc.)" http://genetics.bwh.harvard.edu/pph2/ | ||
| Sift 6.2.1 external sift SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. http://sift.bii.a-star.edu.sg/ |
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The version number here are from Ensembl since we get Polyphen and Sift from vep: https://useast.ensembl.org/info/genome/variation/prediction/protein_function.html
Fix: genome-nexus/genome-nexus#765, GRCh38 updates are in another pr.