Release Version Tool name File name Content Date Retrieved DB Version Number Source (URL) Conversion Script Notes
2012-04 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2012-02-20 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/ see doc/History.txt
2012-04 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2012-02-20 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/ This Ensembl version uses FlyBase FB2010_02 (5.25)
2012-04 v-00 HSEnsgProteinMapper hs-ensg2ensp.tsv Ensembl gene ID to Ensembl protein ID 2012-03-05 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2012-03-05 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2012-03-05 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2012-03-16 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2012-03-19 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2012-03-19 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2012-03-19 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2012-03-19 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2012-03-19 ensembl65 http://dec2011.archive.ensembl.org/biomart/martview/
2012-04 v-00 HSGeneIdConverter hgnc2aliases-2012-02-21.tsv HGNC symbol to HGNC aliases 2012-02-21 N/A http://www.genenames.org/biomart/martview Filters: Record Grouping : primary, Status: Approved
2012-04 v-00 HSEnsgProteinMapper hs-accession2entryname-2012-03-05.tsv UniProt accession code to UniProt entry name 2012-03-05 2012_02 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-03-05.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-03-05.tsv
2012-04 v-01 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2012-03-01 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2012-03-01 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/
This Ensembl version uses FlyBase FB2010_02 (5.25)
2012-04 v-01 HSEnsgProteinMapper hs-ensg2ensp.tsv Ensembl gene ID to Ensembl protein ID 2012-03-05 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2012-03-05 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2012-03-05 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2012-03-16 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2012-03-19 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2012-03-19 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2012-03-19 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2012-03-19 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2012-03-19 ensembl66 http://feb2012.archive.ensembl.org/biomart/martview/

2012-04 v-01 HSGeneIdConverter hgnc2aliases-2012-03-01.tsv HGNC symbol to HGNC aliases 2012-02-21 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2012-04 v-01 HSEnsgProteinMapper hs-accession2entryname-2012-03-05.tsv UniProt accession code to UniProt entry name 2012-03-05 2012_02 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-03-05.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-03-05.tsv
2012-07 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/
This Ensembl version uses FlyBase FB2011_07 (5.39)
2012-07 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSEnsgProteinMapper hs-ensg2ensp.tsv Ensembl gene ID to Ensembl protein ID 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-07 v-00 HSGeneIdConverter hgnc2aliases-2012-05-17.tsv HGNC symbol to HGNC aliases 2012-05-17 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2012-07 v-00 HSEnsgProteinMapper hs-accession2entryname-2012-05-17.tsv UniProt accession code to UniProt entry name 2012-05-17 2012_05 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-05-17.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-05-17.tsv This is release 2012_05 from May 16, 2012. Released after Ensembl 67 was out. Possible minor incompatibilities, as Ensembl will reference into Uniprot 2012_04.
2012-08 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/
This Ensembl version uses FlyBase FB2011_07 (5.39)
2012-08 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSEnsgProteinMapper hs-ensg2ensp.tsv Ensembl gene ID to Ensembl protein ID 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2012-05-17 ensembl67 http://may2012.archive.ensembl.org/biomart/martview/

2012-08 v-00 HSGeneIdConverter hgnc2aliases-2012-05-17.tsv HGNC symbol to HGNC aliases 2012-05-17 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2012-08 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2012-08 v-00 HSEnsgProteinMapper hs-accession2entryname-2012-05-17.tsv UniProt accession code to UniProt entry name 2012-05-17 2012_05 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-05-17.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-05-17.tsv This is release 2012_05 from May 16, 2012. Released after Ensembl 67 was out. Possible minor incompatibilities, as Ensembl will reference into Uniprot 2012_04.
2012-11 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/
This Ensembl version uses FlyBase FB2011_07 (5.39)
2012-11 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSEnsgProteinMapper hs-ensg2ensp.tsv Ensembl gene ID to Ensembl protein ID 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2012-08-16 ensembl68 http://jul2012.archive.ensembl.org/biomart/martview/

2012-11 v-00 HSGeneIdConverter hgnc2aliases-2012-08-16.tsv HGNC symbol to HGNC aliases 2012-08-16 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2012-11 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2012-11 v-00 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2012-11-08.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2012-07-17 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2012-11 v-00 HSEnsgProteinMapper hs-accession2entryname-2012-08-16.tsv UniProt accession code to UniProt entry name 2012-08-16 2012_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-08-16.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-08-16.tsv This is release 2012_07 from Jul 11, 2012. Ensembl and UniProt should be in sync.
2012-11 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2012-11 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2012-11 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-04 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/
This Ensembl version uses FlyBase FB2011_07 (5.39)
2013-04 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-02-14 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/ Newly added.
2013-04 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-02-14 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/ Newly added.
2013-04 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-01-23 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/ Newly added.
2013-04 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/

2013-04 v-00 HSGeneIdConverter hgnc2aliases-2012-08-16.tsv HGNC symbol to HGNC aliases 2012-12-13 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2013-04 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-04 v-00 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2012-11-08.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2012-07-17 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-04 v-00 HSEnsgProteinMapper hs-accession2entryname-2012-08-16.tsv UniProt accession code to UniProt entry name 2012-08-16 2012_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-08-16.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-08-16.tsv This is release 2012_07 from Jul 11, 2012. Ensembl and UniProt should be in sync.
2013-04 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-04 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-04 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2012-12-13 ensembl69 http://oct2012.archive.ensembl.org/biomart/martview/
2013-04 v-00 HGMDAnnotator hd_hgmd_pro_201204 (DB schema) HGMD annotation data base
201204 http://www.hgmd.cf.ac.uk MySQL database.
2013-04 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-04 v-01 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2013-04 v-01 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-02-14 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
2013-04 v-01 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-02-14 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
2013-04 v-01 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-01-23 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
2013-04 v-01 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
2013-04 v-01 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
2013-04 v-01 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/

2013-04 v-01 HSGeneIdConverter hgnc2aliases-2013-01-21.tsv HGNC symbol to HGNC aliases 2013-01-21 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2013-04 v-01 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-04 v-01 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2012-11-08.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2012-07-17 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-04 v-01 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2013-04 v-01 HSEnsgProteinMapper hs-accession2entryname-2013-01-22.tsv UniProt accession code to UniProt entry name 2013-01-22 2013_01 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-08-16.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-08-16.tsv This is release 2013_01 from Jan 9, 2013. Ensembl might lag a bit the UniProt database.
2013-04 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-04 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-04 v-01 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2013-01-21 ensembl70 http://jan2013.archive.ensembl.org/biomart/martview/
2013-04 v-01 HGMDAnnotator hd_hgmd_pro_201204 (DB schema) HGMD annotation data base
201204 http://www.hgmd.cf.ac.uk MySQL database.
2013-04 v-01 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-07 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 -- hs-ensg.tsv Feature table for human Ensembl genes 2013-05-09 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HSGeneIdConverter hgnc2aliases-2013-01-21.tsv HGNC symbol to HGNC aliases 2013-04-19 N/A http://www.genenames.org/biomart/martview Filters: Record Grouping : primary, Status: Approved
2013-07 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-07 v-00 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-07 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2013-07 v-00 HSEnsgProteinMapper hs-accession2entryname-2013-04-19.tsv UniProt accession code to UniProt entry name 2013-04-19 2013_04 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-04-19.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-04-19.tsv This is release 2013_04 from Apr 3, 2013. Ensembl might lag a bit the UniProt database.
2013-07 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-07 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-07 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2013-04-19 ensembl71 http://apr2013.archive.ensembl.org/biomart/martview/
2013-07 v-00 HGMDAnnotator hd_hgmd_pro_201204 (DB schema) HGMD annotation data base
201204 http://www.hgmd.cf.ac.uk MySQL database.
2013-07 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-09 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 -- hs-ensg.tsv Feature table for human Ensembl genes 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HSGeneIdConverter hgnc2aliases-2013-07-08.tsv HGNC symbol to HGNC aliases 2013-07-08 N/A http://www.genenames.org/biomart/martview Filters: Record Grouping : primary, Status: Approved
2013-09 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-09 v-00 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-09 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2013-09 v-00 HSEnsgProteinMapper hs-accession2entryname-2013-07-08.tsv UniProt accession code to UniProt entry name 2013-07-08 2013_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-07-08.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-07-08.tsv This is release 2013_07 from Jun 26, 2013. Ensembl might lag a bit the UniProt database.
2013-09 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-09 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-09 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-00 HGMDAnnotator hd_hgmd_pro_201204 (DB schema) HGMD annotation data base
201204 http://www.hgmd.cf.ac.uk MySQL database.
2013-09 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2013-09 v-00 ClinVarAnnotator clinvar_20130808.tsv NCBI ClinVar data file for mutations of clinical significance 2013-08-08 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20130808.vcf > clinvar_20130808.tsv Used VCF2Dint for conversion.
2013-09 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-09 v-01 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 -- hs-ensg.tsv Feature table for human Ensembl genes 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HSGeneIdConverter hgnc2aliases-2013-07-08.tsv HGNC symbol to HGNC aliases 2013-07-08 N/A http://www.genenames.org/biomart/martview Filters: Record Grouping : primary, Status: Approved
2013-09 v-01 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-09 v-01 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-09 v-01 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2013-09 v-01 HSEnsgProteinMapper hs-accession2entryname-2013-07-08.tsv UniProt accession code to UniProt entry name 2013-07-08 2013_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-07-08.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-07-08.tsv This is release 2013_07 from Jun 26, 2013. Ensembl might lag a bit the UniProt database.
2013-09 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-09 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-09 v-01 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2013-07-08 ensembl72 http://Jun2013.archive.ensembl.org/biomart/martview/
2013-09 v-01 HGMDAnnotator hd_hgmd_pro_201302 (DB schema) HGMD annotation data base
201302 http://www.hgmd.cf.ac.uk MySQL database.
2013-09 v-01 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2013-09 v-01 ClinVarAnnotator clinvar_20130808.tsv NCBI ClinVar data file for mutations of clinical significance 2013-08-08 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20130808.vcf > clinvar_20130808.tsv Used VCF2Dint for conversion.
2013-09 v-01 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-12 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/ This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2013-12 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 -- hs-ensg.tsv Feature table for human Ensembl genes 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2013-10-01 ensembl73 http://sep2013.archive.ensembl.org/biomart/martview/
2013-12 v-00 HSGeneIdConverter hgnc2aliases-2013-10-01.tsv HGNC symbol to HGNC aliases 2013-10-01 N/A http://www.genenames.org/biomart/martview Filters: Record Grouping : primary, Status: Approved
2013-12 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-12 v-00 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-12 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2013-12 v-00 HSEnsgProteinMapper hs-accession2entryname-2013-07-08.tsv UniProt accession code to UniProt entry name 2013-07-08 2013_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2012-07-08.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2012-07-08.tsv
2013-12 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-12 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-12 v-00 HGMDAnnotator hd_hgmd_pro_201302 (DB schema) HGMD annotation data base N/A 201302 http://www.hgmd.cf.ac.uk MySQL database.
2013-12 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2013-12 v-00 ClinVarAnnotator clinvar_20131105.tsv NCBI ClinVar data file for mutations of clinical significance 2013-11-05 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20131105.vcf > clinvar_20131105.tsv Used VCF2Dint for conversion.
2013-12 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-12 v-00 DrugBankAnnotator drugbank-v3-2013-11-04.xsd DrugBank XML schema 2013-11-04 DrugBankV3 http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip Manual edits. Had to add some enumeration types for <xs:element name=”kind”> and remove the “source” enumeration in the paragraph below.
2013-12 v-00 DrugBankAnnotator drugbank-v3-2013-11-04.xml DrugBank XML data 2013-11-04 DrugBankV3 http://www.drugbank.ca/docs/drugbank.xsd
2013-12 v-00 InteractionAnnotator 9606.mitab.06062013_15col.txt IRefIndex MITAB file 2013-06-06 iRefIndexV12
2013-12 v-01 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2013-12 v-01 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSGeneOrthologyMapper hs-dm-pble-orthologs.tsv Putative Ensembl gene ID to flybase gene ID orthology 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/ Manual conversion, format change.
2013-12 v-01 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSGeneOrthologyMapper hs-mm-pble-orthologs.tsv Putative Ensembl gene ID to Ensembl mouse gene ID orthology 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/ Manual conversion, format change.
2013-12 v-01 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSGeneOrthologyMapper hs-ce-pble-orthologs.tsv Putative Ensembl gene ID to worm gene ID orthology 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/ Manual conversion, format change.
2013-12 v-01 -- hs-ensg.tsv Feature table for human Ensembl genes 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2013-12-10 ensembl74 http://dec2013.archive.ensembl.org/biomart/martview/
2013-12 v-01 HSGeneIdConverter hgnc2aliases-2013-12-10.tsv HGNC symbol to HGNC aliases 2013-12-10 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2013-12 v-01 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2013-12 v-01 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2013-12 v-01 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2013-12 v-01 HSEnsgProteinMapper hs-accession2entryname-2013-12-10.tsv UniProt accession code to UniProt entry name 2013-12-10 2013_11 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2013-12-10.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2013-12-10.tsv
2013-12 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2013-12 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2013-12 v-01 HGMDAnnotator hd_hgmd_pro_201302 (DB schema) HGMD annotation data base N/A 201302 http://www.hgmd.cf.ac.uk MySQL database.
2013-12 v-01 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2013-12 v-01 ClinVarAnnotator clinvar_20131105.tsv NCBI ClinVar data file for mutations of clinical significance 2013-11-05 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20131105.vcf > clinvar_20131105.tsv Used VCF2Dint for conversion.
2013-12 v-01 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2013-12 v-01 DrugBankAnnotator drugbank-v3-2013-11-04.xsd DrugBank XML schema 2013-11-04 DrugBankV3 http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip Manual edits. Had to add some enumeration types for <xs:element name=”kind”> and remove the “source” enumeration in the paragraph below.
2013-12 v-01 DrugBankAnnotator drugbank-v3-2013-11-04.xsd DrugBank XML data 2013-11-04 DrugBankV3 http://www.drugbank.ca/docs/drugbank.xsd
2013-12 v-01 InteractionAnnotator 9606.mitab.06062013_15col.txt IRefIndex MITAB file 2013-06-06 iRefIndexV12
2014-03 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2014-03 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh Protein and gene identifiers swapped. WBGene new.
2014-03 v-00 -- hs-ensg.tsv Feature table for human Ensembl genes 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-03 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/
2014-03 v-00 HSGeneIdConverter hgnc2aliases-2014-03-04.tsv HGNC symbol to HGNC aliases 2014-03-04 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2014-03 v-00 SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2014-03 v-00 SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2014-03 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2014-03 v-00 HSEnsgProteinMapper hs-accession2entryname-2013-12-10.tsv UniProt accession code to UniProt entry name 2013-12-10 2013_11 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2013-12-10.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2013-12-10.tsv
2014-03 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2014-03 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2014-03 v-00 HGMDAnnotator hd_hgmd_pro_201304 (DB schema) HGMD annotation data base N/A 201304 http://www.hgmd.cf.ac.uk MySQL database.
2014-03 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2014-03 v-00 ClinVarAnnotator clinvar_20140211.tsv NCBI ClinVar data file for mutations of clinical significance 2014-02-11 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20140211.vcf > clinvar_20140211.tsv Used VCF2Dint for conversion.
2014-03 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2014-03 v-00 DrugBankAnnotator drugbank-v3-2013-11-04.xsd DrugBank XML schema 2013-11-04 DrugBankV3 http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip Manual edits. Had to add some enumeration types for <xs:element name=”kind”> and remove the “source” enumeration in the paragraph below.
2014-03 v-00 DrugBankAnnotator drugbank-v3-2013-11-04.xml DrugBank XML data 2013-11-04 DrugBankV3 http://www.drugbank.ca/docs/drugbank.xsd
2014-03 v-00 InteractionAnnotator 9606.mitab.08122013.txt IRefIndex MITAB file 2014-02-XX iRefIndexV13
2014-08 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2014-08 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 Interval2Genes hs-ensg.tsv Feature table for human Ensembl genes 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-08 v-00 HSGeneIdConverter hgnc2aliases-2014-03-04.tsv HGNC symbol to HGNC aliases 2014-03-04 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2014-08 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2014-08 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2014-08 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2014-08 v-00 HSEnsgProteinMapper hs-accession2entryname-2013-12-10.tsv UniProt accession code to UniProt entry name 2013-12-10 2013_11 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2013-12-10.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2013-12-10.tsv
2014-08 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2014-08 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2014-08 v-00 HGMDAnnotator hd_hgmd_pro_201402 HGMD annotation data base N/A 201402 http://www.hgmd.cf.ac.uk MySQL database.
2014-08 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2014-08 v-00 ClinVarAnnotator clinvar_20140604.tsv NCBI ClinVar data file for mutations of clinical significance 2014-06-04 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20140604.vcf > clinvar_201400604.tsv Used VCF2Dint for conversion.
2014-08 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2014-08 v-00 DrugBankAnnotator drugbank-v4-2014-08-08.xsd DrugBank XML schema 2014-08-08 DrugBankV4 http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip Manual edits. Had to add some enumeration types for <xs:element name=”kind”> and remove the “source” enumeration in the paragraph below.
2014-08 v-00 DrugBankAnnotator drugbank-v4-2014-08-08.xml DrugBank XML data 2014-08-08 DrugBankV4 http://www.drugbank.ca/docs/drugbank.xsd
2014-08 v-00 InteractionAnnotator 9606.mitab.08122013.txt IRefIndex MITAB file 2014-02-XX iRefIndexV13
2014-08 v-00 ReactomeAnnotator Homo_sapiens_biopax3.owl Reactome annotation data base OWL file 2014-07-22 v49 http://www.reactome.org/pages/download-data/

2014-08 v-00 GOAnnotator -- GO annotation data base 2014-07-XX 2014-07 http://archive.geneontology.org/latest-full See INSTALL file. GO graph files are always in sync with this version of GO.
2014-12 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2014-12 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 Interval2Genes hs-ensg.tsv Feature table for human Ensembl genes 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2014-12 v-00 HSGeneIdConverter hgnc2aliases-2014-03-04.tsv HGNC symbol to HGNC aliases 2014-03-04 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2014-12 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2014-12 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2014-12 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2014-12 v-00 HSEnsgProteinMapper hs-accession2entryname-2013-12-10.tsv UniProt accession code to UniProt entry name 2013-12-10 2013_11 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2013-12-10.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2013-12-10.tsv
2014-12 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2014-12 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2014-12 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2014-12-12 VDRC r6.01 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2014-12 v-00 HGMDAnnotator hd_hgmd_pro_201403 HGMD annotation data base 2014-10-20 201403 http://www.hgmd.cf.ac.uk MySQL database.
2014-12 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2014-12 v-00 ClinVarAnnotator clinvar_20140929.tsv NCBI ClinVar data file for mutations of clinical significance 2014-09-29 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20140604.vcf > clinvar_201400604.tsv Used VCF2Dint for conversion.
2014-12 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2014-12 v-00 DrugBankAnnotator drugbank-v4-2014-08-08.xsd DrugBank XML schema 2014-08-08 DrugBankV4 http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip Manual edits. Had to add some enumeration types for <xs:element name=”kind”> and remove the “source” enumeration in the paragraph below.
2014-12 v-00 DrugBankAnnotator drugbank-v4-2014-08-08.xml DrugBank XML data 2014-08-08 DrugBankV4 http://www.drugbank.ca/docs/drugbank.xsd
2014-12 v-00 InteractionAnnotator 9606.mitab.08122013.txt IRefIndex MITAB file 2014-02-XX iRefIndexV13
2014-12 v-00 ReactomeAnnotator Homo_sapiens_biopax3.owl Reactome annotation data base OWL file 2014-07-22 v49 http://www.reactome.org/pages/download-data/

2014-12 v-00 GOAnnotator -- GO annotation data base 2014-07-XX 2014-07 http://archive.geneontology.org/latest-full See INSTALL file. GO graph files are always in sync with this version of GO.
2015-04 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2015-04 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 Interval2Genes hs-ensg.tsv Feature table for human Ensembl genes 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2015-04 v-00 HSGeneIdConverter hgnc2aliases-2014-03-04.tsv HGNC symbol to HGNC aliases 2014-03-04 N/A http://www.genenames.org/biomart/martview
Filters: Record Grouping : primary, Status: Approved
2015-04 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2015-04 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2015-04 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2015-04 v-00 HSEnsgProteinMapper hs-accession2entryname-2015-01-27.tsv UniProt accession code to UniProt entry name 2015-01-27 2015_01 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz zcat idmapping_selected-2015-01-27.tab.gz | awk -F $'\t' '{if( $14=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-2015-01-27.tsv
2015-04 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2015-04 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2015-04 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2014-12-12 VDRC r6.01 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2015-04 v-00 HGMDAnnotator hd_hgmd_pro_201404 HGMD annotation data base 2015-03-03 201404 http://www.hgmd.cf.ac.uk MySQL database.
2015-04 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2015-04 v-00 ClinVarAnnotator clinvar_grch37_20150330.tsv NCBI ClinVar data file for mutations of clinical significance 2015-03-30 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20150303.vcf > clinvar_grch37_20150303.tsv Used VCF2Dint for conversion.
2015-04 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2015-04 v-00 DrugBankAnnotator drugbank-v4-2014-08-08.xsd DrugBank XML schema 2014-08-08 DrugBankV4 http://www.drugbank.ca/system/downloads/current/drugbank.xml.zip Manual edits. Had to add some enumeration types for <xs:element name=”kind”> and remove the “source” enumeration in the paragraph below.
2015-04 v-00 DrugBankAnnotator drugbank-v4-2014-08-08.xml DrugBank XML data 2014-08-08 DrugBankV4 http://www.drugbank.ca/docs/drugbank.xsd
2015-04 v-00 InteractionAnnotator 9606.mitab.08122013.txt IRefIndex MITAB file 2014-02-XX iRefIndexV13
2015-04 v-00 ReactomeAnnotator Homo_sapiens_biopax3.owl Reactome annotation data base OWL file 2014-07-22 v49 http://www.reactome.org/pages/download-data/

2015-04 v-00 GOAnnotator, GOEnricher -- GO annotation data base 2014-07-XX 2014-07 http://archive.geneontology.org/latest-full See INSTALL file. GO graph files are always in sync with this version of GO.
2017-05 v-00 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2012_04 (5.46), see “What's New” in http://jan2013.archive.ensembl.org/Drosophila_melanogaster/Info/Index/
2017-05 v-00 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 Interval2Genes hs-ensg.tsv Feature table for human Ensembl genes 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2014-03-04 ensembl75 http://feb2014.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-00 HSGeneIdConverter hgnc2aliases-2016-08-02.tsv HGNC symbol to HGNC aliases 2016-08-02 N/A http://biomart.genenames.org/martform/#!/default/HGNC?datasets=hgnc_gene_mart awk -F $'\t' '{ printf("%s\t%s\n", $1, $0); }' results.txt | perl ../../../src/perl/cmd/tblsubmerge.pl -H -d $'\t' -s ', ' -u 1 - >hgnc2aliases-2016-08-02.tsv FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2017-05 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker hapmap2-ncbi36-global-ld-2012-07-17.tsv Homo sapiens LD block definition file (HapMap based) 2012-07-17 N/A /home/shared/bioinf/Global_LD/20120717/20120717_ld_blocks_filtered.tsv Just a copy with a more suitable name. Inhouse generated by Daniel Taliun and adapted by Hagen Blankenburg.
2017-05 v-00 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2017-05 v-00 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2017-05 v-00 HSEnsgProteinMapper hs-accession2entryname-2016-08-02.tsv UniProt accession code to UniProt entry name 2016-08-02 2016_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz DATE=”2016-08-02”; curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz >idmapping_selected-$DATE.tab.gz; zcat idmapping_selected-$DATE.tab.gz | awk -F $'\t' '{if( $13=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-$DATE.tsv
2017-05 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2017-05 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2017-05 v-00 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2014-12-12 VDRC r6.01 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2017-05 v-00 HGMDAnnotator hd_hgmd_pro_201602 HGMD annotation data base 2016-07-XX 201602 http://www.hgmd.cf.ac.uk MySQL database.
2017-05 v-00 PharmaADMEntor 20130826-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2013-08-26-pharmaadme/20130826-core-markers.ods
2017-05 v-00 ClinVarAnnotator clinvar_grch37_20160705.tsv NCBI ClinVar data file for mutations of clinical significance 2016-07-05 N/A ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20150303.vcf > clinvar_grch37_20150303.tsv Used VCF2Dint for conversion.
2017-05 v-00 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2017-05 v-00 DrugBankAnnotator drugbank-v5-2016-08-01.xsd DrugBank XML schema 2016-08-01 DrugBankV5.0.1 https://www.drugbank.ca/docs/drugbank.xsd

2017-05 v-00 DrugBankAnnotator drugbank-v5-2016-08-01.xml DrugBank XML data 2016-08-01 DrugBankV5.0.1 http://www.drugbank.ca/releases/5-0-1/downloads/all-full-database
2017-05 v-00 InteractionAnnotator 9606.mitab.04072015.txt IRefIndex MITAB file 2015-04-07 iRefIndexV14
2017-05 v-00 ReactomeAnnotator Homo_sapiens_biopax3.owl Reactome annotation data base OWL file 2016-08-01 v57 http://www.reactome.org/pages/download-data/

2017-05 v-00 GOAnnotator, GOEnricher -- GO annotation data base 2016-07-XX 2016-07 http://archive.geneontology.org/latest-full See INSTALL file. GO graph files are always in sync with this version of GO.
2017-05 v-01 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2014_05 (6.02), see “What's New” in http://mar2016.archive.ensembl.org/Drosophila_melanogaster/Info/Annotation
2017-05 v-01 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 Interval2Genes hs-ensg.tsv Feature table for human Ensembl genes 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2016-07-12 ensembl84 http://mar2016.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-01 HSGeneIdConverter hgnc2aliases-2016-08-02.tsv HGNC symbol to HGNC aliases 2016-08-02 N/A http://biomart.genenames.org/martform/#!/default/HGNC?datasets=hgnc_gene_mart awk -F $'\t' '{ printf("%s\t%s\n", $1, $0); }' results.txt | perl ../../../src/perl/cmd/tblsubmerge.pl -H -d $'\t' -s ', ' -u 1 - >hgnc2aliases-2016-08-02.tsv FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2017-05 v-01 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh38-global-ld-2017-03-30.tsv Homo sapiens LD block definition file (GRCh38 1K Genomes (CEU) based). 2017-03-30 N/A /home/shared/bioinf/Global_LD/20170330/1000genomes-GRCh38-global-ld-2017-03-30.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2017-05 v-01 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (GRCh37 1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2017-05 v-01 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2017-05 v-01 HSEnsgProteinMapper hs-accession2entryname-2016-08-02.tsv UniProt accession code to UniProt entry name 2016-08-02 2016_07 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz DATE=”2016-08-02”; curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz >idmapping_selected-$DATE.tab.gz; zcat idmapping_selected-$DATE.tab.gz | awk -F $'\t' '{if( $13=="9606" ) {printf("%s\t%s\n", $1, $2);}}' >hs-accession2entryname-$DATE.tsv
2017-05 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2017-05 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2017-05 v-01 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2014-12-12 VDRC r6.01 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2017-05 v-01 HGMDAnnotator hd_hgmd_pro_201602 HGMD annotation data base 2016-07-XX 201602 http://www.hgmd.cf.ac.uk MySQL database.
2017-05 v-01 PharmaADMEntor 20160802-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2016-08-02-pharmaadme/20160802-core-markers.ods
2017-05 v-01 ClinVarAnnotator clinvar_grch38_20170131.tsv NCBI ClinVar data file for mutations of clinical significance 2016-07-052017-01-31 2017-01-31 ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20150303.vcf > clinvar_grch37_20150303.tsv Used VCF2Dint for conversion.
2017-05 v-01 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2017-05 v-01 DrugBankAnnotator drugbank-v5-2016-08-01.xsd DrugBank XML schema 2016-08-01 DrugBankV5.0.1 https://www.drugbank.ca/docs/drugbank.xsd

2017-05 v-01 DrugBankAnnotator drugbank-v5-2016-08-01.xml DrugBank XML data 2016-08-01 DrugBankV5.0.1 http://www.drugbank.ca/releases/5-0-1/downloads/all-full-database
2017-05 v-01 InteractionAnnotator 9606.mitab.04072015.txt IRefIndex MITAB file 2015-04-07 iRefIndexV14
2017-05 v-01 ReactomeAnnotator Homo_sapiens_biopax3.owl Reactome annotation data base OWL file 2016-08-01 v59 http://www.reactome.org/pages/download-data/

2017-05 v-01 GOAnnotator, GOEnricher -- GO annotation data base 2016-07-XX 2016-07 http://archive.geneontology.org/latest-full See INSTALL file. GO graph files are always in sync with this version of GO.
2017-05 v-02 HSGeneIdConverter hs-ensg2entrezid.tsv Ensembl gene ID to Entrez gene ID 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh This Ensembl version uses FlyBase FB2014_05 (6.02), see “What's New” in http://mar2017.archive.ensembl.org/Drosophila_melanogaster/Info/Annotation
2017-05 v-02 HSGeneIdConverter hs-ensg2hgncsym.tsv Ensembl gene ID to HGNC symbol 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSEnsgProteinMapper hs-enst2ensp.tsv Ensembl transcript ID to Ensembl protein ID 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSEnsgProteinMapper hs-enst2ccds.tsv Ensembl transcript ID to NCBI CCDS ID 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSEnsgProteinMapper hs-ensg2enst.tsv Ensembl gene ID to Ensembl transcript ID 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSEnsgProteinMapper hs-ensg2uniprotswissprot.tsv Ensembl gene ID to UniProt SwissProt accession code 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSEnsgProteinMapper hs-ensg2uniprottrembl.tsv Ensembl gene ID to UniProt TrEmbl accession code 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSGeneOrthologyMapper hs-dm-orthologs.tsv Ensembl gene ID to flybase gene ID orthology 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSGeneOrthologyMapper hs-mm-orthologs.tsv Ensembl gene ID to Ensembl mouse gene ID orthology 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSGeneOrthologyMapper hs-ce-orthologs.tsv Ensembl gene ID to worm gene ID orthology 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 Interval2Genes hs-ensg.tsv Feature table for human Ensembl genes 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 DMGeneIdConverter dm-fbgn2cgid.tsv Ensembl Fbgn to Flybase CG ID mapping 2017-04-21 ensembl88 http://mar2017.archive.ensembl.org/biomart/martview/ src/misc/fetch-biomart.sh
2017-05 v-02 HSGeneIdConverter hgnc2aliases-2017-04-21.tsv HGNC symbol to HGNC aliases 2017-04-21 N/A http://biomart.genenames.org/martform/#!/default/HGNC?datasets=hgnc_gene_mart awk -F $'\t' '{ printf("%s\t%s\n", $1, $0); }' results.txt | perl ../../../src/perl/cmd/tblsubmerge.pl -H -d $'\t' -s ', ' -u 1 - >hgnc2aliases-2017-04-21.tsv FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2017-05 v-02 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh38-global-ld-2017-03-30.tsv Homo sapiens LD block definition file (GRCh38 1K Genomes (CEU) based). 2017-03-30 N/A /home/shared/bioinf/Global_LD/20170330/1000genomes-GRCh38-global-ld-2017-03-30.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2017-05 v-02 Pos2LDBlock, SNPGeneGlobalLDChecker 1000genomes-GRCh37-global-ld-2013-06-06.tsv Homo sapiens LD block definition file (GRCh37 1K Genomes (CEU) based). 2013-06-06 N/A /home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv Copy. Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2017-05 v-02 HSGeneAtlas hs-geneatlas-2013-02-19.tsv GNF Gene Atlas tissue specific gene expression data 2013-02-19 Affymetrix na33 http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/ ~/projects/eurac/geneatlas2di/BioGPS.py Inhouse generated by Chris X. Weichenberger
2017-05 v-02 HSEnsgProteinMapper hs-accession2entryname-2017-04-21.tsv UniProt accession code to UniProt entry name 2017-04-21 2017_04 ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz DATE="2017-04-21" && curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz -o idmapping_selected-$DATE.tab.gz && zcat idmapping_selected-$DATE.tab.gz | awk -F $'\t' '$13=="9606" {printf("%s\t%s\n", $1, $2);}' >hs-accession2entryname-$DATE.tsv
2017-05 v-02 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.7 Email Thomas Micheler, Tues Jun 5. See comments in the Excel file in directory data/vdrc/r5.7
2017-05 v-02 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2012-09-21 VDRC r5.38 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2017-05 v-02 DMGeneIdConverter trfid2cgid.tsv VDRC transformant ID to FlyBase CG ID 2014-12-12 VDRC r6.01 http://stockcenter.vdrc.at/control/main Copy the two columns from the Excel file. Select 'Download the RNAi library'.
2017-05 v-02 HGMDAnnotator hd_hgmd_pro_201701 HGMD annotation data base 2017-05-XX 201701 http://www.hgmd.cf.ac.uk MySQL database.
2017-05 v-02 PharmaADMEntor 20160802-core-markers.tsv PharmaADME core marker list 2013-08-26 N/A http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=14&Itemid=29 Curated file, see README tab in ~chris/projects/eurac/quickies/2016-08-02-pharmaadme/20160802-core-markers.ods
2017-05 v-02 ClinVarAnnotator clinvar_grch38_20170501.tsv NCBI ClinVar data file for mutations of clinical significance 2017-05-05 2017-05-01 ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/archive_incremental_update/clinvar_20130808.vcf.gz python VCF2Dintegrator.py --add-all --build GRCh37 clinvar_20150303.vcf > clinvar_grch37_20150303.tsv Used VCF2Dint for conversion.
2017-05 v-02 gcoords2cons ebi/condel/20101221/* Condel V2 SIFT/PolyPhen scoring files 2012-11-19 2010-12-21 https://bg.upf.edu/forge/projects/condel/wiki/Download Files should match EnsEMBL abridged version (see Notes) Alternate copy from EnsEMBL Condel plugin: https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel
2017-05 v-02 DrugBankAnnotator Drugbank-v5-2017-04-21.xsd DrugBank XML schema 2016-08-01 DrugBankV5.0.6 https://www.drugbank.ca/docs/drugbank.xsd

2017-05 v-02 DrugBankAnnotator Drugbank-v5-2017-04-21.xml DrugBank XML data 2016-08-01 DrugBankV5.0.6 http://www.drugbank.ca/releases/5-0-6/downloads/all-full-database curl -L -o filename.zip -u EMAIL:PASSWORD https://www.drugbank.ca/releases/5-0-6/downloads/all-full-database
2017-05 v-02 InteractionAnnotator 9606.mitab.04072015.txt IRefIndex MITAB file 2015-04-07 iRefIndexV14
2017-05 v-02 ReactomeAnnotator Homo_sapiens_biopax3_v60 Reactome annotation data base OWL file 2017-05-02 v60 http://www.reactome.org/pages/download-data/

2017-05 v-02 GOAnnotator, GOEnricher -- GO annotation data base 2016-07-XX 2016-07 http://archive.geneontology.org/latest-full See INSTALL file. GO graph files are always in sync with this version of GO.


























































































Tools, if not listed in the “Tool name” column, are usually dependent on the Ensembl release, except they perform pure text manipulations.













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Unchangeable link to 1st occurrence in the whole table, unlikely to change. Gray 10




Text that is linked to by this release/data version block. Black, bold




Link to the first time occurrence of text of this block. Gray 60




Subject to change for every release. Black, no fill