Command Line Interface

biomappings automatically installs the command biomappings. See biomappings --help for usage details.

biomappings

Run the CLI.

Usage

biomappings [OPTIONS] COMMAND [ARGS]...

import

Import external SSSOM files.

Usage

biomappings import [OPTIONS] COMMAND [ARGS]...

biomappings

Import predicted mappings from Biomappings.

Usage

biomappings import biomappings [OPTIONS]

ontoportal

Import uncurated mappings from an OntoPortal instance

Usage

biomappings import ontoportal [OPTIONS] ONTOLOGY_1 ONTOLOGY_2

Options

--instance <instance>

Default:: 'bioportal'
Options:: bioportal | agroportal | ecoportal

Arguments

ONTOLOGY_1: Required argument

ONTOLOGY_2: Required argument

semra

Import raw mappings from SeMRA.

Currently, this workflow is configured to only import semantic mappings from the SeMRA Raw Mapping database (https://doi.org/10.5281/zenodo.11082038) that are not already marked as manual mapping curations, have a CC0 license, and are either an exact match or dbxref.

Note: This command is in preview mode, and functionality may change without warning

Usage

biomappings import semra [OPTIONS]

Options

-p, --prefixes <prefixes>: Filter to mappings whose subject and objects are both in the prefix list.Must pass at least two.

url

Import mappings from a URL.

Usage

biomappings import url [OPTIONS] URL

Arguments

URL: Required argument

lint

Sort files and remove duplicates.

Usage

biomappings lint [OPTIONS]

Options

--strategy <strategy>

Default:: 'passthrough'
Options:: bioregistry | bioregistry-preferred | passthrough

merge

Merge files together to a single SSSOM.

Usage

biomappings merge [OPTIONS]

Options

--sssom-directory <sssom_directory>: Required

ndex

Upload to NDEx.

Usage

biomappings ndex [OPTIONS]

Options

--username <username>: NDEx username, also looks in pystow configuration

--password <password>: NDEx password, also looks in pystow configuration

predict

Predict semantic mappings.

Usage

biomappings predict [OPTIONS] COMMAND [ARGS]...

lexical

Predict semantic mappings with lexical methods.

Usage

biomappings predict lexical [OPTIONS] SOURCE_PREFIX [TARGET_PREFIX]...

Options

-v, --verbose: Enable verbose mode. More -v’s means more verbose.

--relation <relation>: the predicate to assign to semantic mappings

--method <method>

The prediction method to use

Options:: ner | grounding | embedding

--cutoff <cutoff>: The cosine similarity cutoff to use for calling mappings when using embedding predictions

--filter-mutual-mappings: Remove predictions that correspond to already existing mappings in either the subject or object resource

--force: Force re-downloading and re-processing of resources

--force-process: Force re-processing, but not re-downloading of resources

--cache, --no-cache: Should a cache be made

--all-by-all: Don’t just predict from source to targets, but also between all targets

--identifiers-are-names: Consider identifiers as names. This is typical for data models/schemas

-pv, --pin-version <pin_version>: Pin resource versions in PyOBO by giving a pair of prefix + version, such as –pin-version chmo 2025-10-21

Arguments

SOURCE_PREFIX: Required argument

TARGET_PREFIX: Optional argument(s)

summarize

Generate summary charts and tables.

Usage

biomappings summarize [OPTIONS]

Options

--output-directory <output_directory>: Required

--image-directory <image_directory>

test

Test the repository.

Usage

biomappings test [OPTIONS]

Options

--strategy <strategy>

Default:: 'passthrough'
Options:: bioregistry | bioregistry-preferred | passthrough

update

Run all summary, merge, and chart exports.

Usage

biomappings update [OPTIONS]

web

Run the semantic mappings curation app.

Usage

biomappings web [OPTIONS]

Options

--resolver-base <resolver_base>

A custom resolver base URL. Defaults to the Bioregistry.

Default:: 'https://bioregistry.io'

--orcid <orcid>: Your ORCID, if not automatically loadable. Don’t use this with –live-login.

--host <host>

Default:: '127.0.0.1'

--port <port>

Default:: 8775

--eager-persist: If set, will persist after each curation instead of waiting for the commit button to be pushed

--implementation <implementation>

The type of backend for running the curation app. Dict means that data is stored in an in-memory dictionary data structure and SQLite means it uses a database w/ ORM

Default:: 'dict'
Options:: dict | sqlite

--ssl-keyfile <ssl_keyfile>: Path to SSL key file (with the -key.pem extension), which is used to enable the web application to serve HTTPS requests

--ssl-certfile <ssl_certfile>: Path to a SSL certificate file (with the .pem extension) to go along with the key file.

--live-login: Use ORCiD for OAuth-based login

--orcid-client-id <orcid_client_id>: If using –live-login, explicitly set the ORCiD Client ID. Otherwise, loaded via PyStow

--orcid-client-secret <orcid_client_secret>: If using –live-login, explicitly set the ORCiD Client secret. Otherwise, loaded via PyStow

--proxy-fix: If set, sets passthroughs for proxies

--no-open: Turn off automatic webpage opening on app start