Semantic Pydantic

Annotate your data models in Pydantic and APIs in FastAPI with the Bioregistry to make them more FAIR

💪 Getting Started

You can use one of the several extensions to Pydantic and FastAPI's Field classes.

from pydantic import BaseModel, Field

from semantic_pydantic import SemanticField


class Scholar(BaseModel):
    """A model representing a researcher, who might have several IDs on different services."""

    orcid: str = SemanticField(..., prefix="orcid")
    name: str = Field(..., example="Charles Tapley Hoyt")

    wos: str | None = SemanticField(default=None, prefix="wos.researcher")
    dblp: str | None = SemanticField(default=None, prefix="dblp.author")
    github: str | None = SemanticField(default=None, prefix="github")
    scopus: str | None = SemanticField(default=None, prefix="scopus")
    semion: str | None = SemanticField(default=None, prefix="semion")
    publons: str | None = SemanticField(default=None, prefix="publons.researcher")
    authorea: str | None = SemanticField(default=None, prefix="authorea.author")

Similarly, this can be used in FastAPI.

from fastapi import FastAPI
from semantic_pydantic import SemanticPath

app = FastAPI(title="Semantic Pydantic Demo")
Scholar = ...  # defined before


@app.get("/api/orcid/{orcid}", response_model=Scholar)
def get_scholar_from_orcid(orcid: str = SemanticPath(prefix="orcid")):
    """Get xrefs for a researcher in Wikidata, given ORCID identifier."""
    ...  # full implementation in https://github.com/cthoyt/semantic-pydantic
    return Scholar(...)

Here's what the Swagger UI looks like, including all the annotations on both the data model and endpoint arguments.

The demo can be run by cloning the repository, installing its requirements, and running the self-contained demo.py.

🚀 Installation

The most recent code and data can be installed directly from GitHub with:

pip install git+https://github.com/cthoyt/semantic-pydantic.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.