How to cite Ensembl

Question

[Farbod]

Dear Friends, Hi (I am not native in English, So be ready for some . . . )

I have used several Ensembl protein database related to fishes (e.g Zebrafish protein) to check the proteins related to my de novo transcriptome assembly of a non-model fish, using NCBI blastX.

1- How should I cite Ensembl in my paper for these database they have kindly provided?

2- Is there any "Version" that I must mention ? (if yes, where I must find it?)

Thank you

Answer 1

[natasha.sernova]

For example:

http://ensemblgenomes.org/info/publications

http://www.ensembl.org/Help/Faq?id=392 (about Ensemble version)

[Farbod]

Dear natasha.sernova, Hi and thank you.

but it seems that these References are mostly about genome related discoveries and are not about using "Download -> Databases & softwares -> species -> protein"

Am I right ?

Answer 2

[crisime]

They have answered it in their FAQs: http://www.ensembl.org/Help/Faq?id=392

You can find the current version/release on the bottom left of each Ensembl Page.

[LLTommy]

There is a link on the page http://www.ensembl.org/info/about/publications.html

[Farbod]

Hi and thank you

Yes I have seen it before.

[Farbod]

Hi crisime and thanks,

about the Ensembl verion on bottom left of the page, I have check but the protein database of some fishes are un-changed for sometimes, Do I must mention this last Ensembl version that is shown in the Home page ?

[GenoMax]

Or you could mention the version of Ensembl archive where the protein database first appeared, if it has remained unchanged for some time.

[Farbod]

I have used about 14 species Pr database and I think I should mention all of them separately, for example for Zebrafish which one do you suggest?

1- I have used Ensembl zebrafish protein database (GRCz10) for my annotation

2- I have used Ensembl (release-85) zebrafish protein database (GRCz10) for my annotation

3- I have used Ensembl (Yates et al, 2016) zebrafish protein database (GRCz10) for my annotation

Andrew Yates, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla

Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil1 Carlos Garcín Girón, Leo Gordon, Thibaut Hourlier, Sarah E.

Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J. Martin, Thomas

Maurel, William McLaren, Daniel N. Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli,

Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder,

Amonida Zadissa, Ewan Birney, Jennifer Harrow, Matthieu Muffato, Emily Perry, Magali Ruffier, Giulietta Spudich, Stephen

J. Trevanion, Fiona Cunningham, Bronwen L. Aken, Daniel R. Zerbino, Paul Flicek

Ensembl 2016.

Nucleic Acids Res. 2016 44 Database issue:D710-6.

PubMed PMID: 26687719; PubMed CentralPMCID: PMC4702834.

doi:10.1093/nar/gkv1157

[GenoMax]

Cite the paper for Ensembl (10.1093/nar/gkv1157) and then include information about exact database (GRCz10/Release 85) used in your text/tables etc.

[Denise CS]

If I were you, I'd not worry TOO much. Ensembl will not come after you if you do not cite them or if you cite Cunningham et al 2015 instead of Yates et al 2016 (the latest publication). As the Ensembl FAQ has it, the latest Ensembl database paper and the version you've used for the majority of your analyses i.e. Ensembl 85 would be the way forward. The Ensembl database (overall) paper is published every year in the database issue of Nucleic Acid Research (NAR). Ensembl 2017 in NAR should be available by the end of the year. It's great that you appreciate the work by Ensembl and consider citing Ensembl. Not many people do so as services and databases are often taken for granted.

[Farbod]

Dear Denise, Hi and nice to hear from you again,

Thank you for your help, I was looking forward for your suggestion.

and by the way, it is not needed that always "someone come after you" to do the right job.

Take care.

[LLTommy]

Agreed, nobody should come after you to do the right thing. I also want to add that it is simply important to point to the right database as well as the version of it so other people can follow your thoughts. If you publish a paper and just write a database name e.g. Ensembl .... I mean, in 5 years, things might have changed (and most likely have!). So it is in your own interest to point to the version of a database - and obviously you do, so yes, that's the way to go.