annotator¶

Annotation of SBML models.

Handle the XML annotations and notes in SBML. Annotate models from information in annotation csv files. Thereby a model can be fully annotated from information stored in a separate annotation store.

Annotation is performed via searching for ontology terms which describe the model and model components. A standard workflow is looking up the components for instance in things like OLS ontology lookup service.

ExternalAnnotation ¶

ExternalAnnotation(d)

Class for handling SBML annotations defined in external source.

This corresponds to a single entry in the external annotation file. Allows to handle more complex annotation scenarios, e.g. patterns for identifiers.

The columns are

pattern sbml_type annotation_type qualifier resource name

Initialize ExternalAnnotation.

Parameters:

Name	Type	Description	Default
`d`	`dict[str, Any]`	one row of the annotation file, `pattern`, `sbml_type`, `annotation_type` and `resource` are required, `qualifier` and `name` are optional.	required

Raises:

Type	Description
`KeyError`	if a required column is missing
`ValueError`	if a value is not one of the supported choices

check ¶

check()

Check for valid choices.

:raise: ValueError

ModelAnnotator ¶

ModelAnnotator(doc, annotations)

Helper class for annotating SBML models.

Initialize ModelAnnotator.

:param doc: SBMLDocument :param annotations: iterable of ModelAnnotation

annotate_model ¶

annotate_model()

Annotate the model with the given annotations.

This annotates a whole document, so a resource which cannot be canonicalized is reported once for its collection rather than once for every element it is written on, see collect_resource_losses.

get_SBMLQualifier `staticmethod` ¶

get_SBMLQualifier(qualifier_str, qualifier_type)

Lookup of SBMLQualifier for given qualifier string.

:param qualifier_type: BQB or BQM :return: SBML qualifier string

annotate_sbase `staticmethod` ¶

annotate_sbase(sbase, annotation)

Annotate SBase based on given annotation data.

:param sbase: libsbml.SBase :param annotation: Annotation :return:

read_annotations_df `staticmethod` ¶

read_annotations_df(file_path, file_format='*')

Read annotations from given file into DataFrame.

Supports "xlsx", "tsv", "csv", "json", "*"

:param file_path: either path to file, or data in dict format :param file_format: annotation file format :return: pandas.DataFrame

read_annotations `staticmethod` ¶

read_annotations(file_path, file_format='*')

Read annotations from given file into DataFrame.

Supports "xlsx", "tsv", "csv", "json", "*"

:param file_path: either path to file, or data in dict format :param file_format: annotation file format :return: list of annotation objects

collect_resource_losses ¶

collect_resource_losses()

Report the resources written as given once per collection.

An annotation resource which pymetadata cannot canonicalize without changing what it says is written as given, see _resource_for_cvterm. A document can hold tens of thousands of resources of one collection, and what is malformed in one of them is as a rule malformed in all of them. Inside this context each of them is collected and logged as a single warning per collection, in the order of the collection ids; the detail of every single resource is logged at debug. Outside it, every resource is warned about on its own.

The context is entered by the code which writes a whole document. A context inside an active one collects into it and reports nothing of its own, so that a document which is created and then annotated from a file is still reported once.

Returns:

Type	Description
`AbstractContextManager[None]`	the context manager

annotate_sbml ¶

annotate_sbml(source, annotations_path, filepath)

Annotate a given SBML file with the provided annotations.

:param source: SBML to annotation :param annotations_path: external file with annotations :param filepath: annotated SBML file :return: annotated SBMLDocument

annotate_sbml_doc ¶

annotate_sbml_doc(doc, external_annotations)

Annotates given SBML document using the annotations file.

:param doc: SBMLDocument :param external_annotations: ModelAnnotations :return: annotated SBMLDocument