Merge pull request #41 from CMA-Lab/review

Big review of the MTP-DB

Author: MrHedmad

.vscode/settings.json

@@ -9,13 +9,15 @@
         "aquaporins",
         "argparser",
         "assertthat",
+        "biomart",
         "BIOMART",
         "CEPT",
         "colnames",
         "CPUS",
         "dataframes",
         "docstrings",
         "ensembl",
+        "Ensembl",
         "ensg",
         "ensp",
         "entrezgene",
@@ -38,6 +40,7 @@
         "iuphar",
         "lmap",
         "Lysylphosphatidylglycerol",
+        "mazeinspector",
         "mrna",
         "pbar",
         "permeabilities",
@@ -54,20 +57,6 @@
         "transportome",
         "treelib",
         "usefixtures",
-        "wrapattr",
-        "biomart",
-        "colnames",
-        "CPUS",
-        "Ensembl",
-        "executescript",
-        "hardpoint",
-        "hardpoints",
-        "iuphar",
-        "lmap",
-        "pbar",
-        "pqdm",
-        "refseq",
-        "tcdb",
         "wrapattr"
     ],
 }

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Calendar Versioning](https://calver.org/) with the
 ### Changes
 - **BREAKING**: Changed table name from `atp_driven_transporters` to `pumps`.
 - Update run_rebuilder to be compatible with the new CLI;
+- Added tables `structure`, `function` and `origin` with information about the structure, physiological function and tissue of expression of genes.
 - Write better READMEs.
 
 ## [0.23.15-beta] - First release

CONTRIBUTING.md

@@ -12,7 +12,16 @@ If you find a problem, want to point out an error, or have a suggestion or other
 We also use issues to keep track of features that we want in the DB, or things we want to change. Please refer to the [ROADMAP.md](ROADMAP.md) file for the project's roadmap. Feel free to comment on roadmap issues or start working on an item in the roadmap by [creating a fork of the project](https://docs.github.com/en/get-started/quickstart/fork-a-repo).
 
 ## Code style
-We strive to keep a unified code style. For this reason, we use [`pre-commit`](https://pre-commit.com/) to unify the style of our Python code. If you want to contribute code, please make sure you setup the pre-commit hooks with [`pre-commit`](https://pre-commit.com/).
+We strive to keep a unified code style. For this reason, we use [`pre-commit`](https://pre-commit.com/) to unify the style of our Python code. If you want to contribute code, please make sure you setup the pre-commit hooks with [`pre-commit`](https://pre-commit.com/):
+
+```bash
+# For all hooks to be installed, **both** commands must be ran.
+pre-commit install
+pre-commit install -t commit-msg
+```
+
+## Versioning
+We follow follow [CalVer](https://calver.org/) `MAJOR.YY.0W[_MINOR][-Modifier]`. It's a bit weird but the idea is to warn the user immediately if the major version changes.
 
 ## Commit Messages
 We follow the [`conventional commits`](https://www.conventionalcommits.org/en/v1.0.0/) specification.

README.md

@@ -79,3 +79,21 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
 This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+
+
+## Licensing
+
+Daedalus itself and all associated software in this repository is licensed following the [`COPYING`](COPYING) file. We are not sponsored or licensed by any of the data sources that we use.
+
+The data downloaded and parsed by Daedalus is licensed under:
+- The IUPHAR database: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) - Harding SD, Armstrong JF, Faccenda E, Southan C, Alexander SPH, Davenport AP, Pawson AJ, Spedding M, Davies JA; NC-IUPHAR. (2021) The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. Nucl. Acids Res. 2022. 50(D1) D1282-D1294. doi: 10.1093/nar/gkab1010. [Full text](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1010/6414576). PMID: 34718737.
+- The COSMIC database: [Custom License](https://cancer.sanger.ac.uk/license/COSMIC_Non_Commercial_Use_Terms_October2021.pdf). Data is remixed and parsed, so the content of the COSMIC database is not redistributed as-is (which would be forbidden).
+- The Gene Onthology: [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/). Current Zenodo DOI: https://dx.doi.org/10.5281/zenodo.7504797
+- The TCDB: [CC BY 3.0](https://creativecommons.org/licenses/by/3.0/) - Latest publication: Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y, Iddamsetty V, Lam KJK, Tian N, Russum S, Wang J, Medrano-Soto A. (2021). The Transporter Classification Database (TCDB): 2021 update. Nucleic Acids Res. 49(D1):D461-7 [33170213](https://pubmed.ncbi.nlm.nih.gov/33170213/)
+- Ensembl places its data in the Public Domain ([more info](https://www.ensembl.org/info/about/legal/disclaimer.html)).
+- The Human Gene Nomenclature Committee places its data in the Public Domain ([CC0](https://creativecommons.org/share-your-work/public-domain/cc0/), [more info](https://www.genenames.org/about/license/))
+- The Human Protein Atlas: [CC BY 3.0](https://creativecommons.org/licenses/by/3.0/) - Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
+PubMed: 25613900 DOI: 10.1126/science.1260419 ([more info](https://www.proteinatlas.org/about/licence))
+
+
+(Last updated on the 22nd of June, 2023)

src/daedalus/__init__.py

@@ -4,7 +4,8 @@
 from colorama import Back, Fore, Style
 
 __all__ = ["DB_NAME", "SCHEMA"]
-__version__ = "0.23.17-beta"
+# This follows CalVer MAJOR.YEAR.WEEK[.minor][-tag]
+__version__ = "1.23.25-beta"
 
 
 class ColorFormatter(logging.Formatter):

src/daedalus/constants/__init__.py

@@ -10,6 +10,7 @@
     HUGO,
     IUPHAR_COMPILED,
     IUPHAR_DB,
+    PROTEIN_ATLAS,
     SLC_TABLES,
     TCDB,
 )
@@ -30,6 +31,7 @@
     "CACHE_NAME",
     "THESAURUS_FILE",
     "GO",
+    "PROTEIN_ATLAS",
 ]
 
 ## TODO: It could be beneficial to bundle all of these constants into

src/daedalus/constants/url_hardpoints.py

@@ -148,3 +148,10 @@
         "sodium_ion_channels": "GO:0005272",
     },
 }
+
+PROTEIN_ATLAS = {
+    # At the time of writing the site is v23, and we can pinpoint the version by going to
+    # http://v23.proteinatlas.org/ if we want to use just this version.
+    "normal_tissue_expression": "https://www.proteinatlas.org/download/normal_tissue.tsv.zip",
+    "subcellular_location": "https://www.proteinatlas.org/download/subcellular_location.tsv.zip",
+}