Prefix Manager

In KGX, the PrefixManager acts as a central resource for,

  • CURIE to IRI expansion

  • IRI to CURIE contraction

Under the hood, PrefixManager makes use of prefixcommons-py.

Each time the PrefixManager class is initialized, it makes use of the Biolink Model JSON-LD context for a default set of prefix to IRI mappings.

These defaults can be overridden by using update_prefix_map and providing your custom mappings.

kgx.prefix_manager

class kgx.prefix_manager.PrefixManager(url: str | None = None)[source]

Bases: object

Manages prefix mappings.

These include mappings for CURIEs such as GO:0008150, as well as shortforms such as biolink types such as Disease

contract(uri: str, fallback: bool = True) → str | None[source]

Contract a given URI to a CURIE, based on mappings from prefix_map.

Parameters:

  • uri (str) – A URI

  • fallback (bool) – Determines whether to fallback to default prefix mappings, as determined by prefixcommons.curie_util, when URI prefix is not found in reverse_prefix_map.

Returns:

A CURIE corresponding to the URI

Return type:

Optional[str]

expand(curie: str, fallback: bool = True) → str[source]

Expand a given CURIE to an URI, based on mappings from prefix_map.

Parameters:

  • curie (str) – A CURIE

  • fallback (bool) – Determines whether to fallback to default prefix mappings, as determined by prefixcommons.curie_util, when CURIE prefix is not found in prefix_map.

Returns:

A URI corresponding to the CURIE

Return type:

str

static get_prefix(curie: str) → str | None[source]

Get the prefix from a given CURIE.

Parameters:

curie (str) – The CURIE

Returns:

The CURIE prefix

Return type:

str

static get_reference(curie: str) → str | None[source]

Get the reference of a given CURIE.

Parameters:

curie (str) – The CURIE

Returns:

The reference of a CURIE

Return type:

Optional[str]

static is_curie(s: str) → bool[source]

Check if a given string is a CURIE.

Parameters:

s (str) – A string

Returns:

Whether or not the given string is a CURIE

Return type:

bool

static is_iri(s: str) → bool[source]

Check if a given string as an IRI.

Parameters:

s (str) – A string

Returns:

Whether or not the given string is an IRI.

Return type:

bool

set_prefix_map(m: Dict) → None[source]

Populate prefix_map with contents from a JSON-LD context from self.url

Parameters:

m (dict) – Dictionary of prefix to URI mappings

update_prefix_map(m: Dict[str, str]) → None[source]

Update prefix maps with new mappings.

Parameters:

m (Dict) – New prefix to IRI mappings

update_reverse_prefix_map(m: Dict[str, str]) → None[source]

Update reverse prefix maps with new mappings.

Parameters:

m (Dict) – New IRI to prefix mappings