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-2017-04-21.tsv	VDRC transformant ID to FlyBase CG ID	2017-04-21	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	2017-04-21	DrugBankV5.0.6	https://www.drugbank.ca/docs/drugbank.xsd
2017-05	v-02	DrugBankAnnotator	Drugbank-v5-2017-04-21.xml	DrugBank XML data	2017-04-21	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.
2019-01	v-00	HSGeneIdConverter	hs-ensg2entrezid.tsv	Ensembl gene ID to Entrez gene ID	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	This Ensembl version uses FlyBase FB2017_04 (6.17), see in http://Jan2019.archive.ensembl.org/Drosophila_melanogaster/Info/Annotation
2019-01	v-00	HSGeneIdConverter	hs-ensg2hgncsym.tsv	Ensembl gene ID to HGNC symbol	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSEnsgProteinMapper	hs-enst2ensp.tsv	Ensembl transcript ID to Ensembl protein ID	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSEnsgProteinMapper	hs-enst2ccds.tsv	Ensembl transcript ID to NCBI CCDS ID	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSEnsgProteinMapper	hs-ensg2enst.tsv	Ensembl gene ID to Ensembl transcript ID	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSEnsgProteinMapper	hs-ensg2uniprotswissprot.tsv	Ensembl gene ID to UniProt SwissProt accession code	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSEnsgProteinMapper	hs-ensg2uniprottrembl.tsv	Ensembl gene ID to UniProt TrEmbl accession code	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSGeneOrthologyMapper	hs-dm-orthologs.tsv	Ensembl gene ID to flybase gene ID orthology	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSGeneOrthologyMapper	hs-mm-orthologs.tsv	Ensembl gene ID to Ensembl mouse gene ID orthology	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	HSGeneOrthologyMapper	hs-ce-orthologs.tsv	Ensembl gene ID to worm gene ID orthology	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	Interval2Genes	hs-ensg.tsv	Feature table for human Ensembl genes	2019-01-18	ensembl95	http://jan2019.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2019-01	v-00	DMGeneIdConverter	dm-fbgn2cgid.tsv	FlyBase FBgn to annotation ID (CGID) mapping	2019-01-18	FB_2018_06	ftp://ftp.flybase.org/releases/FB2018_06/precomputed_files/genes/fbgn_annotation_ID_fb_2018_06.tsv.gz	zcat fbgn_annotation_ID_fb_2018_06.tsv.gz | awk -F $'\t' '{printf("%s\t%s\n", $3, $5);}' | grep -E $'\tC[GR]' >dm-fbgn2cgid.tsv
2019-01	v-00	HSGeneIdConverter	hgnc2aliases-2019-01-18.tsv	HGNC symbol to HGNC aliases	2019-01-18	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 $'\t' -s ', ' -u 1 - >hgnc2aliases-2019-01-18.tsv	FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2019-01	v-00	Pos2LDBlock, SNPGeneGlobalLDChecker	1000genomes-GRCh38-global-ld-2017-03-30.tsv	Homo sapiens LD block definition file (GRCh38 1K Genomes (CEU) based).	2017-03-30	N/A	/home/shared/bioinf/Global_LD/20170330/1000genomes-GRCh38-global-ld-2017-03-30.tsv	Copy.	Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2019-01	v-00	Pos2LDBlock, SNPGeneGlobalLDChecker	1000genomes-GRCh37-global-ld-2013-06-06.tsv	Homo sapiens LD block definition file (GRCh37 1K Genomes (CEU) based).	2013-06-06	N/A	/home/shared/bioinf/Global_LD/20121108/1000genomes-GRCh37-global-ld-2012-11-08.tsv	Copy.	Inhouse generated by Daniel Taliun and adapted by Chris X. Weichenberger.
2019-01	v-00	HSGeneAtlas	hs-geneatlas-2013-02-19.tsv	GNF Gene Atlas tissue specific gene expression data	2013-02-19	Affymetrix na33	http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133, http://biogps.org/downloads/	~/projects/eurac/geneatlas2di/BioGPS.py	Inhouse generated by Chris X. Weichenberger
2019-01	v-00	HSEnsgProteinMapper	hs-accession2entryname-2019-01-18.tsv	UniProt accession code to UniProt entry name	2019-01-18	2019_01	ftp://ftp.expasy.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz	DATE="2019-01-18" && curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz -o idmapping_selected-$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
2019-01	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
2019-01	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'.
2019-01	v-00	DMGeneIdConverter	trfid2cgid-2019-01-18.tsv	VDRC transformant ID to FlyBase CG ID	2019-01-18	VDRC r6.01	http://stockcenter.vdrc.at/control/main	Copy the two columns from the Excel file.	Select 'Download the RNAi library'.
2019-01	v-00	HGMDAnnotator	hd_hgmd_pro_201701	HGMD annotation data base	2017-05-XX	201701	http://www.hgmd.cf.ac.uk		MySQL database.
2019-01	v-00	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
2019-01	v-00	ClinVarAnnotator	clinvar_grch38_20190118.tsv	NCBI ClinVar data file for mutations of clinical significance	2019-01-18	2019-01-14	ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20190114.vcf.gz	On server: src/misc/replace-clinvar.sh clinvar_20190114.vcf v-00 /home/shared/bioinf/NGSpipeline/data/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly_GRCh38.fasta clinvar_grch38_20190918.tsv	Used VCF2Dint for conversion.
2019-01	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
2019-01	v-00	DrugBankAnnotator	Drugbank-v5-2019-01-18.xsd	DrugBank XML schema	2019-01-18	DrugBankV5.1.2	https://www.drugbank.ca/docs/drugbank.xsd
2019-01	v-00	DrugBankAnnotator	Drugbank-v5-2019-01-18.xml	DrugBank XML data	2019-01-18	DrugBankV5.1.2	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
2019-01	v-00	InteractionAnnotator	9606.mitab.04072015.txt	IRefIndex MITAB file	2015-04-07	iRefIndexV14
2019-01	v-00	ReactomeAnnotator	Homo_sapiens_biopax3_v60	Reactome annotation data base OWL file	2017-05-02	v60	http://www.reactome.org/pages/download-data/
2019-01	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.
2020-06	v-00	HSGeneIdConverter	hs-ensg2entrezid.tsv	Ensembl gene ID to Entrez gene ID	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	There are no archive sites for GRCh37 releases.
2020-06	v-00	HSGeneIdConverter	hs-ensg2hgncsym.tsv	Ensembl gene ID to HGNC symbol	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	HSEnsgProteinMapper	hs-enst2ensp.tsv	Ensembl transcript ID to Ensembl protein ID	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	HSEnsgProteinMapper	hs-enst2ccds.tsv	Ensembl transcript ID to NCBI CCDS ID	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	HSEnsgProteinMapper	hs-ensg2enst.tsv	Ensembl gene ID to Ensembl transcript ID	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	HSEnsgProteinMapper	hs-ensg2uniprotswissprot.tsv	Ensembl gene ID to UniProt SwissProt accession code	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	HSEnsgProteinMapper	hs-ensg2uniprottrembl.tsv	Ensembl gene ID to UniProt TrEmbl accession code	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	HSGeneOrthologyMapper	hs-dm-orthologs.tsv	Ensembl gene ID to flybase gene ID orthology	2020-06-04	ensembl100_38	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	Attention: GRCh37 data is without orthologs.
2020-06	v-00	HSGeneOrthologyMapper	hs-mm-orthologs.tsv	Ensembl gene ID to Ensembl mouse gene ID orthology	2020-06-04	ensembl100_38	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	Attention: GRCh37 data is without orthologs.
2020-06	v-00	HSGeneOrthologyMapper	hs-ce-orthologs.tsv	Ensembl gene ID to worm gene ID orthology	2020-06-04	ensembl100_38	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	Attention: GRCh37 data is without orthologs.
2020-06	v-00	Interval2Genes, HSEnsg2gcoords	hs-ensg.tsv	Feature table for human Ensembl genes	2020-06-04	ensembl100_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-00	DMGeneIdConverter	dm-fbgn2cgid.tsv	FlyBase FBgn to annotation ID (CGID) mapping	2020-06-04	FB_2020_02	ftp://ftp.flybase.org/releases/FB2020_02/precomputed_files/genes/fbgn_annotation_ID_fb_2020_02.tsv.gz	zcat fbgn_annotation_ID_fb_2020_02.tsv.gz | awk -F $'\t' '{printf("%s\t%s\n", $3, $5);}' | grep -E $'\tC[GR]' >dm-fbgn2cgid.tsv
2020-06	v-00	HSGeneIdConverter	hgnc2aliases-2020-06-04.tsv	HGNC symbol to HGNC aliases	2020-06-04	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-2020-06-04.tsv	FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2020-06	v-00	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.
2020-06	v-00	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.
2020-06	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
2020-06	v-00	HSEnsgProteinMapper	hs-accession2entryname-2020-06-04.tsv	UniProt accession code to UniProt entry name	2020-06-04	2020_02	ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz	DATE=2020-06-04 && curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz -o hs_idmap.gz && zcat hs_idmap.gz | grep $'\tUniProtKB-ID\t' | cut -f 1,3 -d $'\t' >hs-accession2entryname-$DATE.tsv	By organism, just 35MB!!
2020-06	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
2020-06	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'.
2020-06	v-00	DMGeneIdConverter	trfid2cgid-2020-06-04.tsv	VDRC transformant ID to FlyBase CG ID	2020-06-04	VDRC r6.01	http://stockcenter.vdrc.at/control/main	Copy the two columns from the Excel file.	Select 'Download the RNAi library'.
2020-06	v-00	HGMDAnnotator	hd_hgmd_pro_201701	HGMD annotation data base	2017-05-XX	201701	http://www.hgmd.cf.ac.uk		MySQL database.
2020-06	v-00	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
2020-06	v-00	ClinVarAnnotator	clinvar_grch37_20200602.tsv.gz	NCBI ClinVar data file for mutations of clinical significance	2020-06-05	2020-06-02	ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20200602.vcf.gz	See src/misc/replace-clinvar.sh [must be done on server]	Used VCF2Dint for conversion.
2020-06	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
2020-06	v-00	DrugBankAnnotator	Drugbank-v5-2020-06-05.xsd	DrugBank XML schema	2020-06-05	DrugBankV5.1.6	https://www.drugbank.ca/docs/drugbank.xsd
2020-06	v-00	DrugBankAnnotator	Drugbank-v5-2020-06-05.xml.gz	DrugBank XML data	2020-06-05	DrugBankV5.1.6	https://www.drugbank.ca/releases/5-1-6/downloads/all-full-database	curl -L -o filename.zip -u EMAIL:PASSWORD https://www.drugbank.ca/releases/5-1-6/downloads/all-full-database
2020-06	v-00	InteractionAnnotator	9606.mitab.04072015.txt	IRefIndex MITAB file	2015-04-07	iRefIndexV14
2020-06	v-00	ReactomeAnnotator	Homo_sapiens_biopax3_v60	Reactome annotation data base OWL file	2017-05-02	v60	http://www.reactome.org/pages/download-data/
2020-06	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.
2020-06	v-01	HSGeneIdConverter	hs-ensg2entrezid.tsv	Ensembl gene ID to Entrez gene ID	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	This Ensembl version uses FlyBase FB2018_03 (6.22), see in http://apr2020.archive.ensembl.org/Drosophila_melanogaster/Info/Annotation
2020-06	v-01	HSGeneIdConverter	hs-ensg2hgncsym.tsv	Ensembl gene ID to HGNC symbol	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSEnsgProteinMapper	hs-enst2ensp.tsv	Ensembl transcript ID to Ensembl protein ID	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSEnsgProteinMapper	hs-enst2ccds.tsv	Ensembl transcript ID to NCBI CCDS ID	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSEnsgProteinMapper	hs-ensg2enst.tsv	Ensembl gene ID to Ensembl transcript ID	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSEnsgProteinMapper	hs-ensg2uniprotswissprot.tsv	Ensembl gene ID to UniProt SwissProt accession code	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSEnsgProteinMapper	hs-ensg2uniprottrembl.tsv	Ensembl gene ID to UniProt TrEmbl accession code	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSGeneOrthologyMapper	hs-dm-orthologs.tsv	Ensembl gene ID to flybase gene ID orthology	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSGeneOrthologyMapper	hs-mm-orthologs.tsv	Ensembl gene ID to Ensembl mouse gene ID orthology	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	HSGeneOrthologyMapper	hs-ce-orthologs.tsv	Ensembl gene ID to worm gene ID orthology	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	Interval2Genes, HSEnsg2gcoords	hs-ensg.tsv	Feature table for human Ensembl genes	2020-06-04	ensembl100_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2020-06	v-01	DMGeneIdConverter	dm-fbgn2cgid.tsv	FlyBase FBgn to annotation ID (CGID) mapping	2020-06-04	FB_2020_02	ftp://ftp.flybase.org/releases/FB2020_02/precomputed_files/genes/fbgn_annotation_ID_fb_2020_02.tsv.gz	zcat fbgn_annotation_ID_fb_2020_02.tsv.gz | awk -F $'\t' '{printf("%s\t%s\n", $3, $5);}' | grep -E $'\tC[GR]' >dm-fbgn2cgid.tsv
2020-06	v-01	HSGeneIdConverter	hgnc2aliases-2020-06-04.tsv	HGNC symbol to HGNC aliases	2020-06-04	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-2020-06-04.tsv	FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2020-06	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.
2020-06	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.
2020-06	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
2020-06	v-01	HSEnsgProteinMapper	hs-accession2entryname-2020-06-04.tsv	UniProt accession code to UniProt entry name	2020-06-04	2020_02	ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz	DATE=2020-06-04 && curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz -o hs_idmap.gz && zcat hs_idmap.gz | grep $'\tUniProtKB-ID\t' | cut -f 1,3 -d $'\t' >hs-accession2entryname-$DATE.tsv	By organism, just 35MB!!
2020-06	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
2020-06	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'.
2020-06	v-01	DMGeneIdConverter	trfid2cgid-2020-06-04.tsv	VDRC transformant ID to FlyBase CG ID	2020-06-04	VDRC r6.01	http://stockcenter.vdrc.at/control/main	Copy the two columns from the Excel file.	Select 'Download the RNAi library'.
2020-06	v-01	HGMDAnnotator	hd_hgmd_pro_201701	HGMD annotation data base	2017-05-XX	201701	http://www.hgmd.cf.ac.uk		MySQL database.
2020-06	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
2020-06	v-01	ClinVarAnnotator	clinvar_grch38_20200602.tsv	NCBI ClinVar data file for mutations of clinical significance	2020-06-05	2020-06-02	ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20200602.vcf.gz	See src/misc/replace-clinvar.sh [must be done on server]	Used VCF2Dint for conversion.
2020-06	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
2020-06	v-01	DrugBankAnnotator	Drugbank-v5-2020-06-05.xsd	DrugBank XML schema	2020-06-05	DrugBankV5.1.6	https://www.drugbank.ca/docs/drugbank.xsd
2020-06	v-01	DrugBankAnnotator	Drugbank-v5-2020-06-05.xml.gz	DrugBank XML data	2020-06-05	DrugBankV5.1.6	https://www.drugbank.ca/releases/5-1-6/downloads/all-full-database	curl -L -o filename.zip -u EMAIL:PASSWORD https://www.drugbank.ca/releases/5-1-6/downloads/all-full-database
2020-06	v-01	InteractionAnnotator	9606.mitab.04072015.txt	IRefIndex MITAB file	2015-04-07	iRefIndexV14
2020-06	v-01	ReactomeAnnotator	Homo_sapiens_biopax3_v60	Reactome annotation data base OWL file	2017-05-02	v60	http://www.reactome.org/pages/download-data/
2020-06	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.
2021-12	v-00	HSGeneIdConverter	hs-ensg2entrezid.tsv	Ensembl gene ID to Entrez gene ID	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	There are no archive sites for GRCh37 releases.
2021-12	v-00	HSGeneIdConverter	hs-ensg2hgncsym.tsv	Ensembl gene ID to HGNC symbol	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	HSEnsgProteinMapper	hs-enst2ensp.tsv	Ensembl transcript ID to Ensembl protein ID	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	HSEnsgProteinMapper	hs-enst2ccds.tsv	Ensembl transcript ID to NCBI CCDS ID	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	HSEnsgProteinMapper	hs-ensg2enst.tsv	Ensembl gene ID to Ensembl transcript ID	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	HSEnsgProteinMapper	hs-ensg2uniprotswissprot.tsv	Ensembl gene ID to UniProt SwissProt accession code	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	HSEnsgProteinMapper	hs-ensg2uniprottrembl.tsv	Ensembl gene ID to UniProt TrEmbl accession code	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	HSGeneOrthologyMapper	hs-dm-orthologs.tsv	Ensembl gene ID to flybase gene ID orthology	2021-12-10	ensembl105_38	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	Attention: GRCh37 data is without orthologs.
2021-12	v-00	HSGeneOrthologyMapper	hs-mm-orthologs.tsv	Ensembl gene ID to Ensembl mouse gene ID orthology	2021-12-10	ensembl105_38	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	Attention: GRCh37 data is without orthologs.
2021-12	v-00	HSGeneOrthologyMapper	hs-ce-orthologs.tsv	Ensembl gene ID to worm gene ID orthology	2021-12-10	ensembl105_38	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	Attention: GRCh37 data is without orthologs.
2021-12	v-00	Interval2Genes, HSEnsg2gcoords	hs-ensg.tsv	Feature table for human Ensembl genes	2021-12-10	ensembl105_37	http://grch37.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-00	DMGeneIdConverter	dm-fbgn2cgid.tsv	FlyBase FBgn to annotation ID (CGID) mapping	2021-12-09	FB_2021_05	ftp://ftp.flybase.org/releases/FB2021_05/precomputed_files/genes/fbgn_annotation_ID_fb_2021_05.tsv.gz	zcat fbgn_annotation_ID_fb_2021_05.tsv.gz | awk -F $'\t' '{printf("%s\t%s\n", $3, $5);}' | grep -E $'\tC[GR]' >dm-fbgn2cgid.tsv
2021-12	v-00	HSGeneIdConverter	hgnc2aliases-2021-12-10.tsv	HGNC symbol to HGNC aliases	2021-12-10	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-2021-12-10.tsv	FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2021-12	v-00	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.
2021-12	v-00	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.
2021-12	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
2021-12	v-00	HSEnsgProteinMapper	hs-accession2entryname-2021-12-10.tsv	UniProt accession code to UniProt entry name	2021-12-10	2021_04	ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz	DATE=2021-12-10 && curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz -o hs_idmap.gz && zcat hs_idmap.gz | grep $'\tUniProtKB-ID\t' | cut -f 1,3 -d $'\t' >hs-accession2entryname-$DATE.tsv	By organism, just 35MB!!
2021-12	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
2021-12	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'.
2021-12	v-00	DMGeneIdConverter	trfid2cgid-2020-06-04.tsv	VDRC transformant ID to FlyBase CG ID	2020-06-04	VDRC r6.01	http://stockcenter.vdrc.at/control/main	Copy the two columns from the Excel file.	Select 'Download the RNAi library'.
2021-12	v-00	HGMDAnnotator	hd_hgmd_pro_201701	HGMD annotation data base	2017-05-XX	201701	http://www.hgmd.cf.ac.uk		MySQL database.
2021-12	v-00	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
2021-12	v-00	ClinVarAnnotator	clinvar_grch37_20211204.tsv.gz	NCBI ClinVar data file for mutations of clinical significance	2021-12-10	2021-12-04	ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20211204.vcf.gz	See src/misc/replace-clinvar.sh [must be done on server]	Used VCF2Dint for conversion.
2021-12	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
2021-12	v-00	DrugBankAnnotator	Drugbank-v5-2021-12-13.xsd	DrugBank XML schema	2020-06-05	DrugBankV5.1.8	https://www.drugbank.ca/docs/drugbank.xsd
2021-12	v-00	DrugBankAnnotator	Drugbank-v5-2021-12-13.xml.gz	DrugBank XML data	2020-06-05	DrugBankV5.1.8	https://www.drugbank.ca/releases/5-1-6/downloads/all-full-database	curl -L -o filename.zip -u EMAIL:PASSWORD https://www.drugbank.ca/releases/5-1-8/downloads/all-full-database
2021-12	v-00	InteractionAnnotator	9606.mitab.06-11-2021.txt.gz	IRefIndex MITAB file	2021-12-13	iRefIndexV18
2021-12	v-00	ReactomeAnnotator	Homo_sapiens_biopax3_v78.gz	Reactome annotation data base OWL file	2021-12-13	v78	http://www.reactome.org/pages/download-data/		Specialized data formats > Events in the BioPAX level 3 format.
2021-12	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.
2021-12	v-01	HSGeneIdConverter	hs-ensg2entrezid.tsv	Ensembl gene ID to Entrez gene ID	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh	This Ensembl version uses FlyBase FB2018_03 (6.22), see in http://apr2020.archive.ensembl.org/Drosophila_melanogaster/Info/Annotation
2021-12	v-01	HSGeneIdConverter	hs-ensg2hgncsym.tsv	Ensembl gene ID to HGNC symbol	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSEnsgProteinMapper	hs-enst2ensp.tsv	Ensembl transcript ID to Ensembl protein ID	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSEnsgProteinMapper	hs-enst2ccds.tsv	Ensembl transcript ID to NCBI CCDS ID	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSEnsgProteinMapper	hs-ensg2enst.tsv	Ensembl gene ID to Ensembl transcript ID	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSEnsgProteinMapper	hs-ensg2uniprotswissprot.tsv	Ensembl gene ID to UniProt SwissProt accession code	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSEnsgProteinMapper	hs-ensg2uniprottrembl.tsv	Ensembl gene ID to UniProt TrEmbl accession code	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSGeneOrthologyMapper	hs-dm-orthologs.tsv	Ensembl gene ID to flybase gene ID orthology	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSGeneOrthologyMapper	hs-mm-orthologs.tsv	Ensembl gene ID to Ensembl mouse gene ID orthology	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	HSGeneOrthologyMapper	hs-ce-orthologs.tsv	Ensembl gene ID to worm gene ID orthology	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	Interval2Genes, HSEnsg2gcoords	hs-ensg.tsv	Feature table for human Ensembl genes	2021-12-10	ensembl105_38	http://apr2020.archive.ensembl.org/biomart/martview/	src/misc/fetch-biomart.sh
2021-12	v-01	DMGeneIdConverter	dm-fbgn2cgid.tsv	FlyBase FBgn to annotation ID (CGID) mapping	2021-12-09	FB_2021_05	ftp://ftp.flybase.org/releases/FB2021_05/precomputed_files/genes/fbgn_annotation_ID_fb_2021_05.tsv.gz	zcat fbgn_annotation_ID_fb_2021_05.tsv.gz | awk -F $'\t' '{printf("%s\t%s\n", $3, $5);}' | grep -E $'\tC[GR]' >dm-fbgn2cgid.tsv
2021-12	v-01	HSGeneIdConverter	hgnc2aliases-2021-12-10.tsv	HGNC symbol to HGNC aliases	2021-12-10	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-2021-12-10.tsv	FILTER -- Status: Approved; ATTRIBUTE -- Approved symbol; Alias symbol
2021-12	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.
2021-12	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.
2021-12	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
2021-12	v-01	HSEnsgProteinMapper	hs-accession2entryname-2021-12-10.tsv	UniProt accession code to UniProt entry name	2021-12-10	2021_04	ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz	DATE=2021-12-10 && curl ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz -o hs_idmap.gz && zcat hs_idmap.gz | grep $'\tUniProtKB-ID\t' | cut -f 1,3 -d $'\t' >hs-accession2entryname-$DATE.tsv	By organism, just 35MB!!
2021-12	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
2021-12	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'.
2021-12	v-01	DMGeneIdConverter	trfid2cgid-2020-06-04.tsv	VDRC transformant ID to FlyBase CG ID	2020-06-04	VDRC r6.01	http://stockcenter.vdrc.at/control/main	Copy the two columns from the Excel file.	Select 'Download the RNAi library'.
2021-12	v-01	HGMDAnnotator	hd_hgmd_pro_201701	HGMD annotation data base	2017-05-XX	201701	http://www.hgmd.cf.ac.uk		MySQL database.
2021-12	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
2021-12	v-01	ClinVarAnnotator	clinvar_grch38_20211204.tsv	NCBI ClinVar data file for mutations of clinical significance	2021-12-10	2021-12-04	ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20211204.vcf.gz	See src/misc/replace-clinvar.sh [must be done on server]	Used VCF2Dint for conversion.
2021-12	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
2021-12	v-01	DrugBankAnnotator	Drugbank-v5-2021-12-13.xsd	DrugBank XML schema	2020-06-05	DrugBankV5.1.8	https://www.drugbank.ca/docs/drugbank.xsd
2021-12	v-01	DrugBankAnnotator	Drugbank-v5-2021-12-13.xml.gz	DrugBank XML data	2020-06-05	DrugBankV5.1.8	https://www.drugbank.ca/releases/5-1-6/downloads/all-full-database	curl -L -o filename.zip -u EMAIL:PASSWORD https://www.drugbank.ca/releases/5-1-8/downloads/all-full-database
2021-12	v-01	InteractionAnnotator	9606.mitab.06-11-2021.txt.gz	IRefIndex MITAB file	2021-12-13	iRefIndexV18
2021-12	v-01	ReactomeAnnotator	Homo_sapiens_biopax3_v78.gz	Reactome annotation data base OWL file	2021-12-13	v78	http://www.reactome.org/pages/download-data/		Specialized data formats > Events in the BioPAX level 3 format.
2021-12	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.
Tools, if not listed in the “Tool name” column, are usually dependent on the Ensembl release, except they perform pure text manipulations.
Legend:
Encoding in table				Color in LibreOffice
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
With the 2020 release, we have references from v-01 to v-00. So any new release should block-copy both releases in one go.