scverse · Elarwei001 · Jun 24, 2026 · Jun 24, 2026 · Jul 9, 2026
diff --git a/docs/src/SUMMARY.md b/docs/src/SUMMARY.md
@@ -10,6 +10,7 @@
 
 # Manual
 * [gget 8cube](en/8cube.md)
+* [gget alliance](en/alliance.md)  
 * [gget alphafold](en/alphafold.md)  
 * [gget archs4](en/archs4.md)
 * [gget bgee](en/bgee.md)
@@ -53,6 +54,7 @@
 
 # Manuál
 * [gget 8cube](es/8cube.md)
+* [gget alliance](es/alliance.md)  
 * [gget alphafold](es/alphafold.md)  
 * [gget archs4](es/archs4.md)  
 * [gget bgee](es/bgee.md)  

diff --git a/docs/src/en/alliance.md b/docs/src/en/alliance.md
@@ -0,0 +1,72 @@
+[<kbd> View page source on GitHub </kbd>](https://github.com/scverse/gget/blob/main/docs/src/en/alliance.md)
+
+> Python arguments are equivalent to long-option arguments (`--arg`), unless otherwise specified. Flags are True/False arguments in Python.  The manual for any gget tool can be called from the command-line using the `-h` `--help` flag.  
+# gget alliance 🧬
+Query the [Alliance of Genome Resources](https://www.alliancegenome.org/), which integrates data from the major model organism databases (human, mouse, rat, zebrafish, fly, worm, yeast, and more).  
+`gget alliance` has two modes, chosen automatically from the input:
+- If the input is an Alliance **gene ID** (e.g. `HGNC:1101`, `MGI:109337`, `RGD:2219`, `ZFIN:...`, `FB:...`, `WB:...`, `SGD:...`), the gene's details are returned.
+- Otherwise, the input is used as a **free-text search** and the matching objects of the given `--category` are returned.
+
+Return format: JSON (command-line) or data frame/CSV (Python).
+
+**Positional argument**  
+`search_term`  
+Alliance gene ID (e.g. `HGNC:1101`) or a free-text search term.
+
+**Optional arguments**  
+`-c` `--category`  
+Category for free-text searches: one of `gene`, `allele`, `disease`, `go`, `variant`, `model`, or `all` for no filter. Default: `gene`.  
+
+`-l` `--limit`  
+Maximum number of results for free-text searches. Default: 10.  
+
+`-o` `--out`  
+Path to the file the results will be saved in, e.g. path/to/directory/results.csv (or .json). Default: Standard out.  
+Python: `save=True` will save the output in the current working directory.
+
+**Flags**  
+`-csv` `--csv`  
+Command-line only. Returns results in CSV format.  
+Python: Use `json=True` to return output in JSON format.
+
+`-q` `--quiet`  
+Command-line only. Prevents progress information from being displayed.  
+Python: Use `verbose=False` to prevent progress information from being displayed.  
+
+### Examples
+**Search for genes across model organisms:**
+```bash
+gget alliance brca2
+```
+```python
+# Python
+gget.alliance("brca2")
+```
+&rarr; Returns a table of genes matching the search term across Alliance member databases.
+
+| id | symbol | name | species | category | so_term_name |
+| --- | --- | --- | --- | --- | --- |
+| HGNC:1101 | BRCA2 | BRCA2 DNA repair associated | Homo sapiens | gene_search_result | protein_coding_gene |
+| MGI:109337 | Brca2 | breast cancer 2 | Mus musculus | gene_search_result | protein_coding_gene |
+
+<br/><br/>
+**Fetch a single gene by its Alliance ID:**
+```bash
+gget alliance HGNC:1101
+```
+```python
+# Python
+gget.alliance("HGNC:1101")
+```
+&rarr; Returns the gene's details.
+
+| id | symbol | name | species | taxon | gene_type | synonyms | data_provider |
+| --- | --- | --- | --- | --- | --- | --- | --- |
+| HGNC:1101 | BRCA2 | BRCA2 DNA repair associated | Homo sapiens | NCBITaxon:9606 | protein_coding_gene | ['FAD', ...] | RGD |
+
+# References
+If you use `gget alliance` in a publication, please cite the following articles:  
+
+- Alliance of Genome Resources Consortium. (2024). Updates to the Alliance of Genome Resources central infrastructure. Genetics. [https://doi.org/10.1093/genetics/iyae049](https://doi.org/10.1093/genetics/iyae049)
+
+- Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. [https://doi.org/10.1093/bioinformatics/btac836](https://doi.org/10.1093/bioinformatics/btac836)
diff --git a/docs/src/en/updates.md b/docs/src/en/updates.md
@@ -5,6 +5,7 @@
 #### *gget* officially became part of [*scverse*](https://scverse.org/) on June 9, 2026. 🥳🥳🥳
 
 **Version ≥ 0.30.9** (XXX XX, 2026):  
+- [`gget alliance`](alliance.md): **New module** to query the [Alliance of Genome Resources](https://www.alliancegenome.org/). Pass an Alliance gene ID (e.g. `HGNC:1101`, `MGI:109337`, `RGD:2219`) to fetch the gene's details, or a free-text term to search genes/alleles/diseases/GO/variants/models across the member model-organism databases (selectable with `category`). Available in the Python API and on the command line.
 
 **Version ≥ 0.30.8** (Jun 28, 2026):  
 - [`gget g2p`](g2p.md): Either `gene` or `--uniprot_id` is now sufficient — whichever is missing is resolved via UniProt and cached. Gene→UniProt picks the canonical reviewed human Swiss-Prot entry; the resolution and its limitations are logged. The canonical pair is **always** prepended to the result as `gene_name` / `uniprot_id` columns (and stored on `df.attrs`), so the output schema is invariant regardless of input mode. Existing call sites continue to work.

diff --git a/docs/src/es/alliance.md b/docs/src/es/alliance.md
@@ -0,0 +1,72 @@
+[<kbd> Ver el codigo fuente de la pagina en GitHub </kbd>](https://github.com/scverse/gget/blob/main/docs/src/es/alliance.md)
+
+> Parámetros de Python són iguales a los parámetros largos (`--parámetro`) de Terminal, si no especificado de otra manera. Banderas son parámetros de verdadero o falso (True/False) en Python. El manuál para cualquier modulo de gget se puede llamar desde la Terminal con la bandera `-h` `--help`.  
+# gget alliance 🧬
+Consulte la [Alliance of Genome Resources](https://www.alliancegenome.org/), que integra datos de las principales bases de datos de organismos modelo (humano, ratón, rata, pez cebra, mosca, gusano, levadura, y más).  
+`gget alliance` tiene dos modos, elegidos automáticamente según la entrada:
+- Si la entrada es un **identificador de gen** de Alliance (p. ej. `HGNC:1101`, `MGI:109337`, `RGD:2219`, `ZFIN:...`, `FB:...`, `WB:...`, `SGD:...`), se devuelven los detalles del gen.
+- De lo contrario, la entrada se usa como una **búsqueda de texto libre** y se devuelven los objetos coincidentes de la `--category` indicada.
+
+Regresa: Resultados en formato JSON (Terminal) o Dataframe/CSV (Python).  
+
+**Parámetro posicional**  
+`search_term`  
+Identificador de gen de Alliance (p. ej. `HGNC:1101`) o un término de búsqueda de texto libre.
+
+**Parámetros opcionales**  
+`-c` `--category`  
+Categoría para las búsquedas de texto libre: una de `gene`, `allele`, `disease`, `go`, `variant`, `model`, o `all` para no filtrar. Por defecto: `gene`.  
+
+`-l` `--limit`  
+Número máximo de resultados para las búsquedas de texto libre. Por defecto: 10.  
+
+`-o` `--out`  
+Ruta al archivo en el que se guardarán los resultados, p. ej. path/to/directory/results.csv (o .json). Por defecto: salida estándar.  
+Python: `save=True` guardará los resultados en el directorio de trabajo actual.  
+
+**Banderas**  
+`-csv` `--csv`  
+Solo Terminal. Devuelve los resultados en formato CSV.  
+Python: Use `json=True` para devolver los resultados en formato JSON.  
+
+`-q` `--quiet`  
+Solo Terminal. Impide que se muestre la información de progreso.  
+Python: Use `verbose=False` para impedir que se muestre la información de progreso.  
+
+### Ejemplos
+**Buscar genes en distintos organismos modelo:**
+```bash
+gget alliance brca2
+```
+```python
+# Python
+gget.alliance("brca2")
+```
+&rarr; Devuelve una tabla de genes que coinciden con el término de búsqueda en las bases de datos miembro de Alliance.
+
+| id | symbol | name | species | category | so_term_name |
+| --- | --- | --- | --- | --- | --- |
+| HGNC:1101 | BRCA2 | BRCA2 DNA repair associated | Homo sapiens | gene_search_result | protein_coding_gene |
+| MGI:109337 | Brca2 | breast cancer 2 | Mus musculus | gene_search_result | protein_coding_gene |
+
+<br/><br/>
+**Obtener un solo gen por su identificador de Alliance:**
+```bash
+gget alliance HGNC:1101
+```
+```python
+# Python
+gget.alliance("HGNC:1101")
+```
+&rarr; Devuelve los detalles del gen.
+
+| id | symbol | name | species | taxon | gene_type | synonyms | data_provider |
+| --- | --- | --- | --- | --- | --- | --- | --- |
+| HGNC:1101 | BRCA2 | BRCA2 DNA repair associated | Homo sapiens | NCBITaxon:9606 | protein_coding_gene | ['FAD', ...] | RGD |
+
+# Referencias
+Si utiliza `gget alliance` en una publicación, por favor cite los siguientes artículos:  
+
+- Alliance of Genome Resources Consortium. (2024). Updates to the Alliance of Genome Resources central infrastructure. Genetics. [https://doi.org/10.1093/genetics/iyae049](https://doi.org/10.1093/genetics/iyae049)
+
+- Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. [https://doi.org/10.1093/bioinformatics/btac836](https://doi.org/10.1093/bioinformatics/btac836)
diff --git a/gget/__init__.py b/gget/__init__.py
@@ -4,6 +4,7 @@
 from importlib.metadata import PackageNotFoundError, version
 
 from .gget_8cube import gene_expression, psi_block, specificity
+from .gget_alliance import alliance
 from .gget_alphafold import alphafold
 from .gget_archs4 import archs4
 from .gget_bgee import bgee

diff --git a/gget/constants.py b/gget/constants.py
@@ -7,6 +7,9 @@
 # strategy avoid hanging indefinitely on slow upstreams.
 DEFAULT_REQUESTS_TIMEOUT = (10, 60)
 
+# Alliance of Genome Resources REST API for gget alliance
+ALLIANCE_URL = "https://www.alliancegenome.org/api"
+
 # Ensembl REST API server for gget seq and info
 ENSEMBL_REST_API = "http://rest.ensembl.org/"
 ENSEMBL_FTP_URL = "http://ftp.ensembl.org/pub/"