scverse · Elarwei001 · Jun 24, 2026 · Jun 24, 2026 · Jul 1, 2026 · Jul 1, 2026
diff --git a/docs/src/SUMMARY.md b/docs/src/SUMMARY.md
@@ -24,6 +24,7 @@
 * [gget g2p](en/g2p.md)
 * [gget gpt](en/gpt.md)  
 * [gget info](en/info.md)  
+* [gget mitocarta](en/mitocarta.md)
 * [gget muscle](en/muscle.md)
 * [gget mutate](en/mutate.md)
 * [gget opentargets](en/opentargets.md)
@@ -67,6 +68,7 @@
 * [gget g2p](es/g2p.md)
 * [gget gpt](es/gpt.md)  
 * [gget info](es/info.md)  
+* [gget mitocarta](es/mitocarta.md)  
 * [gget muscle](es/muscle.md)
 * [gget mutate](es/mutate.md)  
 * [gget opentargets](es/opentargets.md)  

diff --git a/docs/src/en/cite.md b/docs/src/en/cite.md
@@ -67,6 +67,9 @@ Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference data
 
   - The UniProt Consortium , UniProt: the Universal Protein Knowledgebase in 2023, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D523–D531, [https://doi.org/10.1093/nar/gkac1052](https://doi.org/10.1093/nar/gkac1052)
 
+- If using `gget mitocarta`, please also cite:
+  - Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW, Joshi PR, Jourdain AA, Kim SH, Kotrys AV, Lam SS, McCoy JG, Meisel JD, Miranda M, Panda A, Patgiri A, Rogers R, Sadre S, Shah H, Skinner OS, To TL, Walker MA, Wang H, Ward PS, Wengrod J, Yuan CC, Calvo SE, Mootha VK. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res. 2021 Jan 8;49(D1):D1541-D1547. doi: [10.1093/nar/gkaa1011](https://doi.org/10.1093/nar/gkaa1011). PMID: 33174596; PMCID: PMC7779016.
+
 - If using `gget muscle`, please also cite:  
   - Edgar RC (2021), MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping, bioRxiv 2021.06.20.449169. [https://doi.org/10.1101/2021.06.20.449169](https://doi.org/10.1101/2021.06.20.449169)
 

diff --git a/docs/src/en/introduction.md b/docs/src/en/introduction.md
@@ -46,18 +46,23 @@ These are the `gget` core modules. Click on any module to access detailed docume
   </tr>
   <tr>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/info.md"><strong>gget info</strong></a><br><span style="font-size:0.85em;">Fetch all of the information associated with an Ensembl ID.</span></td>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/mitocarta.md"><strong>gget mitocarta</strong></a><br><span style="font-size:0.85em;">Fetch the MitoCarta3.0 inventory of mitochondrial proteins and pathways.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/muscle.md"><strong>gget muscle</strong></a><br><span style="font-size:0.85em;">Align multiple nucleotide or amino acid sequences to each other.</span></td>
-    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/mutate.md"><strong>gget mutate</strong></a><br><span style="font-size:0.85em;">Mutate nucleotide sequences based on specified mutations.</span></td>
   </tr>
   <tr>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/mutate.md"><strong>gget mutate</strong></a><br><span style="font-size:0.85em;">Mutate nucleotide sequences based on specified mutations.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/opentargets.md"><strong>gget opentargets</strong></a><br><span style="font-size:0.85em;">Explore which diseases and drugs a gene is associated with.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/pdb.md"><strong>gget pdb</strong></a><br><span style="font-size:0.85em;">Fetch data from the Protein Data Bank (PDB) based on a PDB ID.</span></td>
-    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/ref.md"><strong>gget ref</strong></a><br><span style="font-size:0.85em;">Get reference genomes from Ensembl.</span></td>
   </tr>
   <tr>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/ref.md"><strong>gget ref</strong></a><br><span style="font-size:0.85em;">Get reference genomes from Ensembl.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/search.md"><strong>gget search</strong></a><br><span style="font-size:0.85em;">Find Ensembl IDs associated with the specified search word.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/seq.md"><strong>gget seq</strong></a><br><span style="font-size:0.85em;">Fetch the nucleotide or amino acid sequence of a gene.</span></td>
+  </tr>
+  <tr>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/en/virus.md"><strong>gget virus</strong></a><br><span style="font-size:0.85em;">Filter and fetch global viral sequences and extensive metadata.</span></td>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"></td>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"></td>
   </tr>
 </table>
 

diff --git a/docs/src/en/mitocarta.md b/docs/src/en/mitocarta.md
@@ -0,0 +1,84 @@
+[<kbd> View page source on GitHub </kbd>](https://github.com/scverse/gget/blob/main/docs/src/en/mitocarta.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 mitocarta 🫀
+Fetch the [MitoCarta3.0](https://www.broadinstitute.org/mitocarta/) inventory of mammalian mitochondrial proteins and pathways from the Broad Institute.  
+Return format: JSON (command-line) or data frame (Python).  
+
+MitoCarta3.0 is a curated inventory of genes encoding proteins with strong support of mitochondrial localization, annotated with sub-mitochondrial localization and pathway membership.
+
+The returned table is *tidy* (analysis-ready) rather than the raw Excel: delimited columns — `Synonyms` and `MitoCarta3.0_MitoPathways`, plus the pathways table's `Genes` — are split into lists, which become nested arrays in JSON output.
+
+> `gget mitocarta` needs the optional `xlrd` dependency to read MitoCarta's `.xls` file. Install it with `pip install gget[mitocarta]`.
+
+**Optional arguments**  
+`-s` `--species`  
+Species to fetch: `human` (default) or `mouse`.  
+
+`-w` `--which`  
+Which table to return. Default: `mitocarta`.  
+`mitocarta` - The MitoCarta3.0 inventory of mitochondrial genes (one row per mitochondrial gene, with sub-mitochondrial localization, MitoPathways, evidence, and scores).  
+`all_genes` - All genes scored for mitochondrial localization (Maestro scores), not only the mitochondrial ones.  
+`pathways`  - The MitoPathways hierarchy and the list of genes in each pathway.  
+
+`-o` `--out`  
+Path to the file the results will be saved in, e.g. path/to/directory/results.json (or .csv). 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 instead of JSON.  
+Python: Use `json=True` to return a list of dictionaries instead of a data frame.  
+
+`-q` `--quiet`  
+Command-line only. Prevents progress information from being displayed.  
+Python: Use `verbose=False` to prevent progress information from being displayed.  
+
+
+### Examples
+
+**Fetch the human MitoCarta3.0 mitochondrial gene inventory:**  
+```bash
+gget mitocarta --species human --csv
+```
+```python
+# Python
+import gget
+gget.mitocarta(species="human", which="mitocarta")
+```
+&rarr; Returns the ~1,100 human mitochondrial genes and their MitoCarta3.0 annotations (sub-mitochondrial localization, MitoPathways, evidence, scores).
+
+| HumanGeneID | Symbol | Description    | MitoCarta3.0_List | MitoCarta3.0_SubMitoLocalization | MitoCarta3.0_MitoPathways               |
+|-------------|--------|----------------|-------------------|----------------------------------|-----------------------------------------|
+| 1537        | CYC1   | cytochrome c1  | 1                 | MIM                              | OXPHOS > Complex&nbsp;III&nbsp;assembly |
+| 6390        | SDHB   | ...            | 1                 | MIM                              | OXPHOS, Metabolism                      |
+
+<br/><br/>
+
+**Fetch the MitoPathways hierarchy and their genes:**  
+```bash
+gget mitocarta --which pathways --csv
+```
+```python
+# Python
+gget.mitocarta(which="pathways")
+```
+&rarr; Returns the MitoPathways and the genes assigned to each pathway.
+
+<br/><br/>
+
+**JSON output.** The command line returns JSON by default (use `--csv` for CSV; in Python use `json=True` for a list of dictionaries). List columns are emitted as arrays:
+```json
+[
+  {
+    "MitoPathway": "Mitochondrial central dogma",
+    "MitoPathways Hierarchy": "Mitochondrial central dogma",
+    "Genes": ["AARS2", "ALKBH1", "ANGEL2", "APEX1", "..."]
+  }
+]
+```
+
+# References
+If you use `gget mitocarta` in a publication, please cite the following article:  
+
+- Rath S, Sharma R, Gupta R, et al. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res. 2021 Jan 8;49(D1):D1541-D1547. doi: [10.1093/nar/gkaa1011](https://doi.org/10.1093/nar/gkaa1011). PMID: 33174596; PMCID: PMC7779016.
diff --git a/docs/src/en/updates.md b/docs/src/en/updates.md
@@ -5,6 +5,9 @@
 #### *gget* officially became part of [*scverse*](https://scverse.org/) on June 9, 2026. 🥳🥳🥳
 
 **Version ≥ 0.30.9** (XXX XX, 2026):  
+- [`gget mitocarta`](mitocarta.md): **New module** to fetch the [MitoCarta3.0](https://www.broadinstitute.org/mitocarta/) inventory of mammalian mitochondrial proteins and pathways from the Broad Institute (resolves [issue 118](https://github.com/scverse/gget/issues/118)).
+  - Supports human and mouse via the `species` argument; the `which` argument returns the mitochondrial gene inventory (`mitocarta`, default), all genes with Maestro localization scores (`all_genes`), or the MitoPathways hierarchy and their genes (`pathways`).
+  - Returns a `pandas` DataFrame (or a list of dictionaries / JSON with `json=True`). Adds `xlrd` as a dependency to read the MitoCarta Excel file.
 
 **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/cite.md b/docs/src/es/cite.md
@@ -67,6 +67,9 @@ Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference data
 
   - The UniProt Consortium , UniProt: the Universal Protein Knowledgebase in 2023, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D523–D531, [https://doi.org/10.1093/nar/gkac1052](https://doi.org/10.1093/nar/gkac1052)
 
+- Si utiliza `gget mitocarta`, favor de citar también:
+  - Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW, Joshi PR, Jourdain AA, Kim SH, Kotrys AV, Lam SS, McCoy JG, Meisel JD, Miranda M, Panda A, Patgiri A, Rogers R, Sadre S, Shah H, Skinner OS, To TL, Walker MA, Wang H, Ward PS, Wengrod J, Yuan CC, Calvo SE, Mootha VK. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res. 2021 Jan 8;49(D1):D1541-D1547. doi: [10.1093/nar/gkaa1011](https://doi.org/10.1093/nar/gkaa1011). PMID: 33174596; PMCID: PMC7779016.
+
 - Si utiliza `gget muscle`, favor de citar también:  
   - Edgar RC (2021), MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping, bioRxiv 2021.06.20.449169. [https://doi.org/10.1101/2021.06.20.449169](https://doi.org/10.1101/2021.06.20.449169)
 

diff --git a/docs/src/es/introduction.md b/docs/src/es/introduction.md
@@ -47,18 +47,23 @@ Estos son los módulos principales de `gget`. Haga clic en cualquier módulo par
   </tr>
   <tr>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/info.md"><strong>gget info</strong></a><br><span style="font-size:0.85em;">Recuperar toda la información asociada con un ID de Ensembl.</span></td>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/mitocarta.md"><strong>gget mitocarta</strong></a><br><span style="font-size:0.85em;">Obtener el inventario MitoCarta3.0 de proteínas y vías mitocondriales.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/muscle.md"><strong>gget muscle</strong></a><br><span style="font-size:0.85em;">Alinear múltiples secuencias de nucleótidos o aminoácidos entre sí.</span></td>
-    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/mutate.md"><strong>gget mutate</strong></a><br><span style="font-size:0.85em;">Mutar secuencias de nucleótidos según mutaciones específicas.</span></td>
   </tr>
   <tr>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/mutate.md"><strong>gget mutate</strong></a><br><span style="font-size:0.85em;">Mutar secuencias de nucleótidos según mutaciones específicas.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/opentargets.md"><strong>gget opentargets</strong></a><br><span style="font-size:0.85em;">Explorar qué enfermedades y medicamentos están asociados con un gen.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/pdb.md"><strong>gget pdb</strong></a><br><span style="font-size:0.85em;">Recuperar datos de la Base de Datos de Proteínas (PDB) según un ID de PDB.</span></td>
-    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/ref.md"><strong>gget ref</strong></a><br><span style="font-size:0.85em;">Obtener genomas de referencia de Ensembl.</span></td>
   </tr>
   <tr>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/ref.md"><strong>gget ref</strong></a><br><span style="font-size:0.85em;">Obtener genomas de referencia de Ensembl.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/search.md"><strong>gget search</strong></a><br><span style="font-size:0.85em;">Encontrar IDs de Ensembl asociados con la palabra de búsqueda especificada.</span></td>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/seq.md"><strong>gget seq</strong></a><br><span style="font-size:0.85em;">Recuperar la secuencia de nucleótidos o aminoácidos de un gen.</span></td>
+  </tr>
+  <tr>
     <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"><a href="/gget/es/virus.md"><strong>gget virus</strong></a><br><span style="font-size:0.85em;">Filtrar y obtener secuencias virales globales y metadatos extensos.</span></td>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"></td>
+    <td style="width:33.33%; padding:20px; text-align:center; vertical-align:top;"></td>
   </tr>
 </table>
 

diff --git a/docs/src/es/mitocarta.md b/docs/src/es/mitocarta.md
@@ -0,0 +1,84 @@
+[<kbd> Ver el codigo fuente de la pagina en GitHub </kbd>](https://github.com/scverse/gget/blob/main/docs/src/es/mitocarta.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 mitocarta 🫀
+Obtenga el inventario [MitoCarta3.0](https://www.broadinstitute.org/mitocarta/) de proteínas y vías mitocondriales de mamíferos del Broad Institute.  
+Regresa: JSON (línea de comandos) o un data frame (Python).  
+
+MitoCarta3.0 es un inventario curado de genes que codifican proteínas con fuerte respaldo de localización mitocondrial, anotados con la localización submitocondrial y la pertenencia a vías.
+
+La tabla que se regresa está *ordenada* (*tidy*, lista para análisis) en lugar del Excel sin procesar: las columnas delimitadas — `Synonyms` y `MitoCarta3.0_MitoPathways`, además de la columna `Genes` de la tabla de vías — se dividen en listas, que se convierten en arreglos anidados en la salida JSON.
+
+> `gget mitocarta` necesita la dependencia opcional `xlrd` para leer el archivo `.xls` de MitoCarta. Instálala con `pip install gget[mitocarta]`.
+
+**Parámetros optionales**  
+`-s` `--species`  
+Especie a obtener: `human` (por defecto) o `mouse`.  
+
+`-w` `--which`  
+Qué tabla regresar. Por defecto: `mitocarta`.  
+`mitocarta` - El inventario MitoCarta3.0 de genes mitocondriales (una fila por gen mitocondrial, con localización submitocondrial, MitoPathways, evidencia, y puntuaciones).  
+`all_genes` - Todos los genes puntuados para localización mitocondrial (puntuaciones Maestro), no solo los mitocondriales.  
+`pathways`  - La jerarquía de MitoPathways y la lista de genes en cada vía.  
+
+`-o` `--out`  
+Ruta al archivo en el que se guardarán los resultados, p. ej. ruta/al/directorio/resultados.json (o .csv). Por defecto: salida estándar (STDOUT).  
+Para Python, usa `save=True` para guardar los resultados en el directorio de trabajo actual.  
+
+**Banderas**  
+`-csv` `--csv`  
+Solo para Terminal. Produce los resultados en formato CSV en lugar de JSON.  
+Para Python, usa `json=True` para producir una lista de diccionarios en lugar de un data frame.  
+
+`-q` `--quiet`  
+Solo para Terminal. Impide la información de progreso de ser exhibida durante la ejecución del programa.  
+Para Python, usa `verbose=False` para impedir la información de progreso de ser exhibida durante la ejecución del programa.  
+
+
+### Ejemplos
+
+**Obtenga el inventario de genes mitocondriales MitoCarta3.0 humano:**  
+```bash
+gget mitocarta --species human --csv
+```
+```python
+# Python
+import gget
+gget.mitocarta(species="human", which="mitocarta")
+```
+&rarr; Regresa los ~1,100 genes mitocondriales humanos y sus anotaciones MitoCarta3.0 (localización submitocondrial, MitoPathways, evidencia, puntuaciones).
+
+| HumanGeneID | Symbol | Description    | MitoCarta3.0_List | MitoCarta3.0_SubMitoLocalization | MitoCarta3.0_MitoPathways               |
+|-------------|--------|----------------|-------------------|----------------------------------|-----------------------------------------|
+| 1537        | CYC1   | cytochrome c1  | 1                 | MIM                              | OXPHOS > Complex&nbsp;III&nbsp;assembly |
+| 6390        | SDHB   | ...            | 1                 | MIM                              | OXPHOS, Metabolism                      |
+
+<br/><br/>
+
+**Obtenga la jerarquía de MitoPathways y sus genes:**  
+```bash
+gget mitocarta --which pathways --csv
+```
+```python
+# Python
+gget.mitocarta(which="pathways")
+```
+&rarr; Regresa los MitoPathways y los genes asignados a cada vía.
+
+<br/><br/>
+
+**Salida JSON.** La línea de comandos regresa JSON por defecto (usa `--csv` para CSV; en Python usa `json=True` para una lista de diccionarios). Las columnas de tipo lista se emiten como arreglos:
+```json
+[
+  {
+    "MitoPathway": "Mitochondrial central dogma",
+    "MitoPathways Hierarchy": "Mitochondrial central dogma",
+    "Genes": ["AARS2", "ALKBH1", "ANGEL2", "APEX1", "..."]
+  }
+]
+```
+
+# Citar
+Si utiliza `gget mitocarta` en una publicación, favor de citar el siguiente artículo:  
+
+- Rath S, Sharma R, Gupta R, et al. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res. 2021 Jan 8;49(D1):D1541-D1547. doi: [10.1093/nar/gkaa1011](https://doi.org/10.1093/nar/gkaa1011). PMID: 33174596; PMCID: PMC7779016.