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Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 EnsemblCrossReference

Source Notebook

Look up Ensembl identifiers or external symbols and provide cross references in other databases

Contributed by: Keiko Hirayama

ResourceFunction["EnsemblCrossReference"][id]

looks up id and retrieves its cross references.

ResourceFunction["EnsemblCrossReference"]["DatabasesBySpecies"]

retrieves the list of supported databases by species.

Details and Options

ResourceFunction["EnsemblCrossReference"] is based on Ensembl, which provides genomics information including genes, transcripts and proteins.
ResourceFunction["EnsemblCrossReference"] performs lookups of Ensembl Identifiers or external symbols and returns their references in other databases.
The argument id can be an Ensembl identifier, a symbol and accession number of an external database or a list of these.
The following options can be given:
"Species""human"species for which to query; should be one of selected TaxonomicSpecies entities or names of species; use EnsemblCrossReference["DatabasesBySpecies"] to get the list supported species
"Database"Allspecifies from which to retrieve references; use EnsemblCrossReference["DatabasesBySpecies"] to get the list supported databases

Examples

Basic Examples (3) 

Retrieve cross references for an Ensembl gene:

In[1]:=
ResourceFunction[ "EnsemblCrossReference", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["ENSG00000030110"]
Out[1]=

Retrieve cross references for a specified gene symbol:

In[2]:=
ResourceFunction[ "EnsemblCrossReference", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["BRCA2"]
Out[2]=

Find the list of supported external databases by species:

In[3]:=
ResourceFunction[ "EnsemblCrossReference", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["DatabasesBySpecies"]
Out[3]=

Scope (1) 

For ambiguous identifiers, EnsemblCrossReference looks up all potential references that match the identifier:

In[4]:=
ResourceFunction[ "EnsemblCrossReference", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["7157"]
Out[4]=

Options (2) 

Species (1) 

Use the "Species" option to specify the organism to query about:

In[5]:=
ResourceFunction[ "EnsemblCrossReference", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["BRCA2", {"Species" -> Entity["TaxonomicSpecies", "MusMusculus::y84t7"]}]
Out[5]=

Database (1) 

Use the "Database" option to specify the database from which to retrieve the cross reference:

In[6]:=
ResourceFunction[ "EnsemblCrossReference", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["BRCA2", {"Database" -> "HGNC"}]
Out[6]=

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.0.1 – 21 April 2025
  • 1.0.0 – 04 April 2025

Source Metadata

  • Citation:
    • Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De Silva, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Dionysios Grigoriadis, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Tatiana A Gurbich, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Disha Lodha, Diego Marques-Coelho, Gareth Maslen, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, José G Pérez-Silva, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Dan Sheppard, Swati Sinha, Botond Sipos, Vasily Sitnik, William Stark, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Doreen Ware, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Fiona Cunningham, Sarah Dyer, Robert D Finn, Fergal J Martin, and Andrew D Yates
      Ensembl 2024 Nucleic Acids Res. 2024, 52(D1):D891–D899 PMID: 37953337

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