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

 

### 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Withdrawn;status_opt=3;=on;where=;order_by=gd_app_sym_sort;limit=;format=text;submit=submit;.cgifields=;.cgifields=status;.cgifields=chr'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}
   
 

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