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pyneuroml.annotations module#

Methods related to annotations

File: pyneuroml/annotations.py

Copyright 2024 NeuroML contributors

pyneuroml.annotations.create_annotation(subject, title=None, abstract=None, annotation_style: Literal['miriam', 'biosimulations'] = 'biosimulations', description: str | None = None, keywords: List[str] | None = None, thumbnails: List[str] | None = None, organisms: Dict[str, str] | None = None, encodes_other_biology: Dict[str, str] | None = None, has_version: Dict[str, str] | None = None, is_version_of: Dict[str, str] | None = None, has_part: Dict[str, str] | None = None, is_part_of: Dict[str, str] | None = None, has_property: Dict[str, str] | None = None, is_property_of: Dict[str, str] | None = None, sources: Dict[str, str] | None = None, is_instance_of: Dict[str, str] | None = None, has_instance: Dict[str, str] | None = None, predecessors: Dict[str, str] | None = None, successors: Dict[str, str] | None = None, see_also: Dict[str, str] | None = None, references: Dict[str, str] | None = None, other_ids: Dict[str, str] | None = None, citations: Dict[str, str] | None = None, authors: Dict[str, str] | None = None, contributors: Dict[str, str] | None = None, license: Dict[str, str] | None = None, funders: Dict[str, str] | None = None, creation_date: str | None = None, modified_dates: List[str] | None = None, serialization_format: str = 'pretty-xml', write_to_file: str | None = None)#

Create an RDF annotation from the provided fields

Added in version 1.2.10.

This can be used to create an RDF annotation for a subject—a model or a file like an OMEX archive file. It supports most qualifiers and will be continuously updated to support more as they are added.

It merely uses rdflib to make life easier for users to create annotations by coding in the various predicates for each subject.

For information on the specifications, see:

Note that:

  • not all qualifiers have been included yet

  • the qualifiers and their representations may change in the future

For any arguments here that take a dictionary of strings, the key is the resource reference URI, and the value is the string label. For example:

encodes_other_biology={
    "http://identifiers.org/GO:0009653": "anatomical structure morphogenesis",
    "http://identifiers.org/kegg:ko04111": "Cell cycle - yeast",
}
Parameters:

  • subject (str) – subject/target of the annotation could be a file, a mode component

  • title (str) – title of annotation This is required for publishing models on biosimulations.org

  • abstract (str) – an abstract

  • annotation_style (str) –

    type of annotation: either “miriam” or “biosimulations” (default).

    There’s a difference in the annotation “style” suggested by MIRIAM and Biosimulations. MIRIAM suggests the use of RDF containers (bags) wherewas Biosimulations does not. This argument allows the user to select what style they want to use for the annotation.

  • description (str) – a longer description

  • keywords (list(str)) – keywords

  • thumbnails (list(str)) – thumbnails

  • organisms (dict(str, str)) – of organisms

  • encodes_other_biology (dict(str, str)) – other biological entities

  • has_version (dict(str, str)) – other versions

  • is_version_of (dict(str, str)) – is a version of

  • has_part (dict(str, str)) – includes another as a part

  • is_part_of (dict(str, str)) – is a part of another entity

  • has_property (dict(str, str)) – has a property

  • is_property_of (dict(str, str)) – is a property of another entity

  • sources (dict(str, str)) – links to sources (on GitHub and so on)

  • is_instance_of (dict(str, str)) – is an instance of

  • has_instance (dict(str, str)) – has instance of another entity

  • predecessors (dict(str, str)) – predecessors of this entity

  • successors (dict(str, str)) – successors of this entity

  • see_also (dict(str, str)) – more information

  • references (dict(str, str)) – references

  • other_ids (dict(str, str)) – other IDs

  • citations (dict(str, str)) – related citations

  • authors (dict(str, str)) – authors

  • contributors (dict(str, str)) – other contributors

  • license (dict(str, str)) – license

  • funders (dict(str, str)) – funders

  • creation_date (str) – date in YYYY-MM-DD format when this was created (eg: 2024-04-19)

  • modified_dates (list(str)) – dates in YYYY-MM-DD format when modifications were made

  • serialization_format (str) – format to serialize in using rdflib.serialize

  • write_to_file (str) – path to file to write to

Returns:

the annotation string in the requested format.

pyneuroml.annotations.extract_annotations(nml2_file: str) → None#

Extract and print annotations from a NeuroML 2 file.

Parameters:

nml2_file (str) – name of NeuroML2 file to parse

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