Merge pull request #97 from leexgh/grch38-update-hgnc-202410

Update HGNC to 202410 for GRCh38

data/common_input/version_info.txt

@@ -1,15 +1,31 @@
 name	version	type	id	genome_build	description	url
 VEP	grch37	mirrored	vep	grch37	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
 VEP	grch38	mirrored	vep	grch38	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://useast.ensembl.org/info/docs/tools/vep/index.html
-HGNC	2023-10	mirrored	hgnc	grch37	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	2023-10	mirrored	hgnc	grch38	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	grch37	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	grch38	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/
 Cancer Hotspots	v2	mirrored	cancer_hotspots	grch37	A resource for statistically significant mutations in cancer 	https://www.cancerhotspots.org
 Cancer Hotspots	v2	mirrored	cancer_hotspots	grch38	A resource for statistically significant mutations in cancer 	https://www.cancerhotspots.org
 3D Hotspots	v2	mirrored	3d_hotspots	grch37	A resource for statistically significant mutations clustering in 3d protein structures in cancer	https://www.3dhotspots.org/
 3D Hotspots	v2	mirrored	3d_hotspots	grch38	A resource for statistically significant mutations clustering in 3d protein structures in cancer	https://www.3dhotspots.org/
-reVUE	https://github.com/knowledgesystems/reVUE-data/blob/main/VUEs.json	mirrored	revue	grch37	A Repository for Variants with Unexpected Effects (VUE) in Cancer	https://www.cancerrevue.org/
-Mutation Assessor	v3	mirrored	mutation_assessor	grch37	Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms.	http://mutationassessor.org/r3/
+reVUE	https://github.com/knowledgesystems/reVUE-data/blob/main/generated/VUEs.json	mirrored	revue	grch37	A Repository for Variants with Unexpected Effects (VUE) in Cancer	https://www.cancerrevue.org/
 My Variant Info	Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html	external	my_variant_info	grch37	MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources.	https://myvariant.info
 My Variant Info	Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html	external	my_variant_info	grch38	MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources.	https://myvariant.info
-ClinVar	20230722	mirrored	clinvar	grch37	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
-ClinVar	20230722	mirrored	clinvar	grch38	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
+ClinVar	20250106	mirrored	clinvar	grch37	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
+ClinVar	20250106	mirrored	clinvar	grch38	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
+OncoKB	v4.24	mirrored	oncokb	grch37	OncoKB™ is a precision oncology knowledge base that contains biological and clinical information about genomic alterations in cancer.	https://www.oncokb.org/
+OncoKB	v4.24	mirrored	oncokb	grch38	OncoKB™ is a precision oncology knowledge base that contains biological and clinical information about genomic alterations in cancer.	https://www.oncokb.org/
+PDB	latest	external	pdb	grch37	A resource for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids.	https://www.rcsb.org/
+PDB	latest	external	pdb	grch38	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	grch37	Xref endpoint is a lookup of Ensembl Identifiers and retrieve their external references in other databases	http://grch37.rest.ensembl.org/
+xrefs	latest	external	xrefs	grch38	Xref endpoint is a lookup of Ensembl Identifiers and retrieve their external references in other databases	http://grch37.rest.ensembl.org/
+PFAM	32	mirrored	pfam	grch37	A database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.	https://www.ebi.ac.uk/interpro/
+PFAM	32	mirrored	pfam	grch38	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	grch37	A resource for protein post-translational modifications (PTMs).	https://awi.cuhk.edu.cn/dbPTM/
+PTM	dbPTM 2019	mirrored	ptm	grch38	A resource for protein post-translational modifications (PTMs).	https://awi.cuhk.edu.cn/dbPTM/
+SignalDB	https://www.nature.com/articles/s41588-021-00949-1	mirrored	signal	grch37	The SIGNAL resource integrates germline and somatic alterations identified by clinical sequencing of active cancer patients. 	https://www.signaldb.org/
+Polyphen-2	2.2.3, release 405c	external	polyphen	grch37	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/
+Polyphen-2	2.2.3, release 405c	external	polyphen	grch38	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	grch37	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/
+Sift	6.2.1	external	sift	grch38	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/
+Mutation Assessor	v4	mirrored	mutation_assessor	grch37	"Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms."	http://mutationassessor.org/r3/
+Mutation Assessor	v4	mirrored	mutation_assessor	grch38	"Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms."	http://mutationassessor.org/r3/

data/grch37_ensembl92/export/annotation_version.txt

@@ -6,7 +6,7 @@ Cancer Hotspots	v2	mirrored	cancer_hotspots	A resource for statistically signifi
 reVUE	https://github.com/knowledgesystems/reVUE-data/blob/main/generated/VUEs.json	mirrored	revue	A Repository for Variants with Unexpected Effects (VUE) in Cancer	https://www.cancerrevue.org/
 My Variant Info	"Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html"	external	my_variant_info	"MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources."	https://myvariant.info
 ClinVar	20250106	mirrored	clinvar	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
-OncoKB	v4.24	mirrored	oncokb	OncoKB is a precision oncology knowledge base that contains biological and clinical information about genomic alterations in cancer.	https://www.oncokb.org/
+OncoKB	v4.24	mirrored	oncokb	OncoKB™ is a precision oncology knowledge base that contains biological and clinical information about genomic alterations in cancer.	https://www.oncokb.org/
 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/

data/grch38_ensembl92/export/annotation_version.txt

@@ -1,8 +1,15 @@
 name	version	type	id	description	url
 VEP	grch38	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://useast.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/
 Cancer Hotspots	v2	mirrored	cancer_hotspots	A resource for statistically significant mutations in cancer 	https://www.cancerhotspots.org
 3D Hotspots	v2	mirrored	3d_hotspots	A resource for statistically significant mutations clustering in 3d protein structures in cancer	https://www.3dhotspots.org/
 My Variant Info	Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html	external	my_variant_info	MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources.	https://myvariant.info
-ClinVar	20230722	mirrored	clinvar	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
-OncoKB	v4.24	mirrored	oncokb	OncoKB™ is a precision oncology knowledge base that contains biological and clinical information about genomic alterations in cancer.	https://www.oncokb.org/
+ClinVar	20250106	mirrored	clinvar	ClinVar aggregates information about genomic variation and its relationship to human health.	https://www.ncbi.nlm.nih.gov/clinvar/
+OncoKB	v4.24	mirrored	oncokb	OncoKB™ is a precision oncology knowledge base that contains biological and clinical information about genomic alterations in cancer.	https://www.oncokb.org/
+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	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/
+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/
+Mutation Assessor	v4	mirrored	mutation_assessor	Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms.	http://mutationassessor.org/r3/