prefixmaps 0.1.0

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prefixmaps

A python library for retrieving semantic prefix maps

A semantic prefix map will map a a prefix (e.g. skos) to a namespace (e.g http://www.w3.org/2004/02/skos/core#)

This library is designed to satisfy the following requirements

• coverage of prefixes from multiple different domains
• multiple authorities
• preferred semantic namespace is prioritized over web URLs
• authority preferred prefix is prioritized
• lightweight
• network-independence
• versioned prefix maps
• ability to retrieve latest from external authority on network

Installation

pip install prefixmaps

Usage

to use in combination with curies library:

from prefixmaps.io.parser import load_context, load_multi_context
from curies import Converter

ctxt = load_multi_context(["obo", "bioregistry.upper", "linked_data", "prefixcc"])
converter = Converter.from_prefix_map(ctxt.as_dict())

>>> converter.expand("CHEBI:1")
'http://purl.obolibrary.org/obo/CHEBI_1'
>>> converter.expand("GEO:1")
'http://purl.obolibrary.org/obo/GEO_1'
>>> converter.expand("owl:Class")
'http://www.w3.org/2002/07/owl#Class'
>>> converter.expand("FlyBase:FBgn123")
'http://identifiers.org/fb/FBgn123'

Refresh

By default this will make use of metadata distributed alongside the package. This has certain advantages in terms of reproducibility, but it means if a new ontology or prefix is added to an upstream source you won't see this.

To refresh and use the latest upstream:

ctxt = load_context("obo", refresh=True)

Order

order is significant - sources listed first will take priority. The as_dict method ensures that the map is bijective

Contexts

See contexts.curated.yaml

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