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chores: clean current implementation by removing unneeded files
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‎.gitignore‎

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notebooks/cache/
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.venv/
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‎api_view_user.md‎

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# API final view from user perspective
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## Importing the library
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- Complete import of Ontograph
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```python
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import ontograph
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```
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## Download Ontologies
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- Download a single ontology from standard resources
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```python
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resource = [
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{"name_id": "go","format": "obo"},
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]
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path_ontologie = ontograph.downloader.download(resource, cache_directory)
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```
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- Download a multiple ontologies from standard resources
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```python
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resources = [
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{"name_id": "go","format": "obo"},
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{"name_id": "chebi","format": "owl"},
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]
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paths_ontologies = ontograph.downloader.download(resources, cache_directory)
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```
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## Load ontologies
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- Load the "ontology from standard resources, or local source"
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```python
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gene_ontology = ontograph.load(name_id="go", format="obo")
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```
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## Exploring the ontology
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- Print the metadata related to the ontology
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```python
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gene_ontology.metadata()
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```
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- Print the roots of the ontology
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```python
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gene_ontology.roots()
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```
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```mermaid
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flowchart TD
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%% API Layer
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A1[OntologyClient<br>api/client.py]
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%% Core Domain
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subgraph Core
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B1[OntologyGraph<br>core/ontology_graph.py]
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B2[QueryEngine<br>core/query_engine.py]
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B3[TermMapping<br>core/term_mapping.py]
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end
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%% Ports (Interfaces)
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subgraph Ports
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P1[OntologyLoader<br>ports/ontology_loader.py]
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P2[GraphBackend<br>ports/graph_backend.py]
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P3[Downloader<br>ports/downloader.py]
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end
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%% Adapters
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subgraph Adapters
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C1[pronto_loader.py]
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C2[pronto_graph.py]
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C3[pooch_downloader.py]
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C4[tsv_mapping_loader.py]
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end
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%% Utilities & Config (internal use only)
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subgraph Utils_Config
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U1[file_cache.py]
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U2[validation.py]
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U3[logging.py]
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S1[settings.py]
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end
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%% Connections
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A1 --> B1
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A1 --> B2
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A1 --> B3
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%% Core uses Ports (interfaces)
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B1 --> P1
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B2 --> P2
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B3 --> P3
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%% Adapters implement Ports (interfaces)
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P1 -.-> C1
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P2 -.-> C2
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P3 -.-> C3
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P3 -.-> C4
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%% Internal usage (no direct arrow from API)
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Core --> Utils_Config
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Adapters --> Utils_Config
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```
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**Legend:**
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- --> means "uses"
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- -.-> means "implemented by"

‎notebooks/template_notebooks.ipynb‎

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},
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{
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"cell_type": "code",
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"execution_count": 45,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import pronto\n",
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"\n",
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"# 3. Local application/library specific imports\n",
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"from ontograph.downloader import download_file\n",
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"import ontograph.constants as constants"
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"from ontograph._downloader import download_file\n",
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"import ontograph._constants as _constants"
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Downloading data from 'https://purl.obolibrary.org/obo/go.obo' to file '/home/ecarreno/SSC-Projects/b_REPOSITORIES/ontograph/notebooks/cache/gene_ontology.obo'.\n",
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"100%|█████████████████████████████████████| 35.1M/35.1M [00:00<00:00, 97.7GB/s]\n",
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"SHA256 hash of downloaded file: 0908af70601dd41f2c55f664ca5d5959e939162362e9a5573c6794b5d850e601\n",
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"Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Gene Ontology OBO file cached at: /home/ecarreno/SSC-Projects/b_REPOSITORIES/ontograph/notebooks/cache/gene_ontology.obo\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"CACHE_DIRECTORY = \"cache\"\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": 76,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 75,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 77,
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Format_version: \n",
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"\t1.2\n",
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"Data_version: \n",
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"\treleases/2025-06-01\n",
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"Ontology_identifier: \n",
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"\tgo\n",
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"Last_update: \n",
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"\tNone\n",
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"Name: \n",
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"\tGene Ontology\n",
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"Description: \n",
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"\tThe Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.\n",
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"License: \n",
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"\thttp://creativecommons.org/licenses/by/4.0/\n",
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"Roots: \n",
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"\t['GO:0003674', 'GO:0005575', 'GO:0008150']\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"print_metadata(gene_ontology)"
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]
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"\n",
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"Include citations for any external content or suggested resources for deeper learning."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Added to sys.path: /home/edwin/SSC-Projects/b_REPOSITORIES/ontograph\n"
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]
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}
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],
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"source": [
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"import sys\n",
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"import os\n",
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"\n",
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"# Get the absolute path to the parent folder (where both 'notebooks' and 'ontograph' live)\n",
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"project_root = os.path.abspath(os.path.join(os.getcwd(), \"..\"))\n",
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"\n",
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"# Insert at front of sys.path so it's prioritized\n",
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"sys.path.insert(0, project_root)\n",
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"\n",
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"print(\"Added to sys.path:\", project_root)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Downloading data from 'http://purl.obolibrary.org/obo/go.obo' to file '/home/edwin/.ontograph_cache/go.obo'.\n",
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"SHA256 hash of downloaded file: 0908af70601dd41f2c55f664ca5d5959e939162362e9a5573c6794b5d850e601\n",
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"Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"{'name': 'go', 'version': 'releases/2025-06-01', 'format': '1.2'}\n"
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]
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},
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{
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"ename": "AttributeError",
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"evalue": "'Ontology' object has no attribute 'roots'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[3], line 7\u001b[0m\n\u001b[1;32m 4\u001b[0m gene_ontology \u001b[38;5;241m=\u001b[39m client\u001b[38;5;241m.\u001b[39mload(name_id\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mgo\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28mformat\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mobo\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 6\u001b[0m \u001b[38;5;28mprint\u001b[39m(gene_ontology\u001b[38;5;241m.\u001b[39mmetadata())\n\u001b[0;32m----> 7\u001b[0m \u001b[38;5;28mprint\u001b[39m([root\u001b[38;5;241m.\u001b[39mid \u001b[38;5;28;01mfor\u001b[39;00m root \u001b[38;5;129;01min\u001b[39;00m \u001b[43mgene_ontology\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mroots\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m])\n",
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"File \u001b[0;32m~/SSC-Projects/b_REPOSITORIES/ontograph/ontograph/api/client.py:51\u001b[0m, in \u001b[0;36mOntologyWrapper.roots\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 50\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21mroots\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m---> 51\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43montology\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mroots\u001b[49m())\n",
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"\u001b[0;31mAttributeError\u001b[0m: 'Ontology' object has no attribute 'roots'"
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]
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}
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],
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"source": [
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"from ontograph.api.client import OntologyClient\n",
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"\n",
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"client = OntologyClient()\n",
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"gene_ontology = client.load(name_id=\"go\", format=\"obo\")\n",
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"\n",
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"print(gene_ontology.metadata())\n",
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"print([root.id for root in gene_ontology.roots()])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"print(os.listdir(sys.path[0]))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import ontograph.api.client\n",
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"\n",
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"\n",
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"ontograph.api."
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "ontograph",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.12"
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"version": "3.10.18"
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}
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},
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"nbformat": 4,

‎ontograph/adapters/obo_foundry_registry.py‎

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if __name__ == "__main__":
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# Define the path to store the registry
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path = Path("./")
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path = Path("./data/out")
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# Create object registry
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obo_reg = OBOFoundryRegistry(cache_dir=path)

‎ontograph/constants.py‎

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