GeneNomenclatureUtils_download_urls.txt（生物信息学数据库数据下载链接）

最新推荐文章于 2024-10-13 10:27:20 发布

转载最新推荐文章于 2024-10-13 10:27:20 发布 · 1.5k 阅读

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本文提供了从多个权威数据库下载基因和蛋白质命名资源的指南。涵盖了Mouse Genome Informatics (MGI)、HGNC、Entrez Gene、OMIM、Rat Genome Database (RGD) 和 UniProt等数据库的下载链接及说明。

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### Community-provided gene and protein nomenclature resources utilised by the

### GeneNomenclatureUtils packages

### Mouse Genome Informatics (MGI) ###

wget ftp://ftp.informatics.jax.org/pub/reports/HMD_HumanPhenotype.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/HMD_HGNC_Accession.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MGI_MouseHumanSequence.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_Synonym.sql.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_InterPro.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MGI_InterProDomains.sql.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/gene_association.mgi

wget ftp://ftp.informatics.jax.org/pub/reports/VOC_MammalianPhenotype.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenoGenoMP.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_Sequence.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_SwissProt.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_SwissProt_TrEMBL.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_Reference.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_VEGA.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/MRK_ENSEMBL.rpt

wget ftp://ftp.informatics.jax.org/pub/reports/HMD_HumanSequence.rpt

### HGNC ###

wget -O hgnc_core_data.txt 'http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Core+Data;col=gd_hgnc_id;col=gd_app_sym;col=gd_app_name;col=gd_status;col=gd_prev_sym;col=gd_aliases;col=gd_pub_chrom_map;col=gd_pub_acc_ids;col=gd_pub_refseq_ids;status=Approved;status=Approved+Non-Human;status=Entry+Withdrawn;status_opt=3;=on;where=;order_by=gd_app_sym_sort;limit=;format=text;submit=submit;.cgifields=;.cgifields=status;.cgifields=chr'

wget -O hgnc_all_data.txt 'http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=All+Data;col=gd_hgnc_id;col=gd_app_sym;col=gd_app_name;col=gd_status;col=gd_locus_type;col=gd_prev_sym;col=gd_prev_name;col=gd_aliases;col=gd_pub_chrom_map;col=gd_date2app_or_res;col=gd_date_mod;col=gd_date_name_change;col=gd_pub_acc_ids;col=gd_enz_ids;col=gd_pub_eg_id;col=gd_mgd_id;col=gd_other_ids;col=gd_pubmed_ids;col=gd_pub_refseq_ids;col=gd_gene_fam_name;col=md_gdb_id;col=md_eg_id;col=md_mim_id;col=md_refseq_id;col=md_prot_id;status=Approved;status=Approved+Non-Human;status=Entry+Withdrawn;status_opt=3;=on;where=;order_by=gd_app_sym_sort;limit=;format=text;submit=submit;.cgifields=;.cgifields=status;.cgifields=chr'

### Entrez Gene ###

wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz

wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz

wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz

wget ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene

wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene2pubmed.gz

wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz

### OMIM files not available from NCBI 2/11 ###

# wget ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z

# wget ftp://ftp.ncbi.nih.gov/repository/OMIM/genemap

# wget ftp://ftp.ncbi.nih.gov/repository/OMIM/genemap.key

# wget ftp://ftp.ncbi.nih.gov/repository/OMIM/morbidmap

### Using archived OMIM NCBI files ###

wget ftp://ftp.ncbi.nih.gov/repository/OMIM/ARCHIVE/omim.txt.Z

wget ftp://ftp.ncbi.nih.gov/repository/OMIM/ARCHIVE/genemap

wget ftp://ftp.ncbi.nih.gov/repository/OMIM/ARCHIVE/genemap.key

wget ftp://ftp.ncbi.nih.gov/repository/OMIM/ARCHIVE/morbidmap

### Rat Genome Database (RGD) ###

wget ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN.txt

wget ftp://rgd.mcw.edu/pub/data_release/GENES_MOUSE.txt

wget ftp://rgd.mcw.edu/pub/data_release/GENES_RAT.txt

wget ftp://rgd.mcw.edu/pub/data_release/RGD_ORTHOLOGS

### UniProt ###

wget ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz

wget ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz

# setenv RGD_dir ${cwd}

# setenv MGI_dir ${cwd}

# setenv ENTREZ_dir ${cwd}

# setenv HGNC_dir ${cwd}

# setenv OMIM_dir ${cwd}

# setenv NCBI_dir ${cwd}

# setenv SWISS_dir ${cwd}