HELP: old BridgeDb gene/protein ID mapping files

[Egon Willighagen]

Hi all,

During the December 2019 cyberattack, we lost some of the Ensembl 91 ID mapping files (yes, future releases will be archived properly).

The following files got missing, and the first one particular is badly needed by someone now.

#Sus scrofa idmapper-pgdb:/opt/bridgedb-databases/Ss_Derby_Ensembl_91.bridge

#Aspergillus niger idmapper-pgdb:/opt/bridgedb-databases/An_Derby_Ensembl_Fungi_39.bridge
#Ciona intestinalis idmapper-pgdb:/opt/bridgedb-databases/Ci_Derby_Ensembl_91.bridge
#Glycine max idmapper-pgdb:/opt/bridgedb-databases/Gm_Derby_Ensembl_Plant_39.bridge
#Hordeum vulgare idmapper-pgdb:/opt/bridgedb-databases/Hv_Derby_Ensembl_Plant_39.bridge
#Macaca mulatta idmapper-pgdb:/opt/bridgedb-databases/Ml_Derby_Ensembl_91.bridge
#Mycobacterium tuberculosis idmapper-pgdb:/opt/bridgedb-databases/Mx_Derby_Ensembl_91.bridge
#Ornithorhynchus anatinus idmapper-pgdb:/opt/bridgedb-databases/Oa_Derby_Ensembl_91.bridge
#Oryza sativa Indica idmapper-pgdb:/opt/bridgedb-databases/Oi_Derby_Ensembl_Plant_39.bridge
#Populus trichocarpa idmapper-pgdb:/opt/bridgedb-databases/Pi_Derby_Ensembl_Plant_39.bridge
#Equus caballus idmapper-pgdb:/opt/bridgedb-databases/Qc_Derby_Ensembl_91.bridge
#Solanum lycopersicum idmapper-pgdb:/opt/bridgedb-databases/Sl_Derby_Ensembl_Plant_39.bridge
#Vitis vinifera idmapper-pgdb:/opt/bridgedb-databases/Vv_Derby_Ensembl_Plant_39.bridge
#Xenopus tropicalis idmapper-pgdb:/opt/bridgedb-databases/Xt_Derby_Ensembl_91.bridge

Does anyone have any of these files on some old harddisk? Your help is very much appreciated!

We are in the process of building new mapping files, but with all the development of the past 3 years in BridgeDb and changes in fields in Ensembl, we have not completed this yet. Soon we hope.

Egon

--

This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer Nature. See https://twitter.com/egonwillighagen/status/1403299501947899907 

-----

E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)

Twitter/Mastodon: @egonwillighagen / @egonw
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

[Alexander Pico]

I do not. Anders found Ss_Derby_Ensembl_85.bridge if that’s helpful?

 - Alex

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[Anders Riutta]

Hi Egon,

In addition to the files I mentioned yesterday, I also have access to the following files:

On my laptop:

interactions_20180425.bridge

On data.wikipathways.eqiad1.wikimedia.cloud at /data/project/databases/ :

Ag_Derby_Ensembl_Metazoa_39.bridge
An_Derby_Ensembl_Fungi_32.bridge
At_Derby_Ensembl_Plant_39.bridge
Bs_Derby_Ensembl_91.bridge
Bt_Derby_Ensembl_91.bridge
Ce_Derby_Ensembl_91.bridge
Cf_Derby_Ensembl_91.bridge
Ci_Derby_Ensembl_85.bridge
Dm_Derby_Ensembl_91.bridge
Dr_Derby_Ensembl_91.bridge
Ec_Derby_Ensembl_91.bridge
gdb.config
Gg_Derby_Ensembl_91.bridge
Gm_Derby_Ensembl_Plant_32.bridge
Gz_Derby_Ensembl_Fungi_39.bridge
Hs_Derby_Ensembl_91.bridge
Hv_Derby_Ensembl_Plant_32.bridge
Ml_Derby_Ensembl_85.bridge
Mm_Derby_Ensembl_91.bridge
Mx_Derby_Ensembl_85.bridge
Oa_Derby_Ensembl_85.bridge
Oi_Derby_Ensembl_Plant_32.bridge
Oj_Derby_Ensembl_Plant_39.bridge
Pi_Derby_Ensembl_Plant_32.bridge
Pt_Derby_Ensembl_91.bridge
Qc_Derby_Ensembl_85.bridge
Rn_Derby_Ensembl_91.bridge
Sc_Derby_Ensembl_91.bridge
Sl_Derby_Ensembl_Plant_32.bridge
Ss_Derby_Ensembl_85.bridge
Vv_Derby_Ensembl_Plant_32.bridge
Xt_Derby_Ensembl_85.bridge
Zm_Derby_Ensembl_Plant_39.bridge

-Anders

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--

Anders Riutta

anders...@gladstone.ucsf.edu | Bioinformatics Core | Institute of Data Science and Biotechnology

Gladstone Institutes | Science Overcoming Disease

[Egon Willighagen]

On Wed, Oct 27, 2021 at 1:25 AM Alexander Pico <xande...@gmail.com> wrote:

I do not. Anders found Ss_Derby_Ensembl_85.bridge if that’s helpful?

Yes, it very much was. They are now available at our BridgeDb ID mapping file download page, except when we already had a newer file:

https://bridgedb.github.io/data/gene_database/

Thanks, Anders!

Egon