sbmlutils.metadata.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.

Module Contents

Classes

ExternalAnnotation

Class for handling SBML annotations defined in external source.

ModelAnnotator

Helper class for annotating SBML models.

Functions

annotate_sbml(source, annotations_path, filepath)

Annotate a given SBML file with the provided annotations.

annotate_sbml_doc(doc, external_annotations)

Annotates given SBML document using the annotations file.

Attributes

logger

sbmlutils.metadata.annotator.logger[source]
sbmlutils.metadata.annotator.annotate_sbml(source, annotations_path, filepath)[source]

Annotate a given SBML file with the provided annotations.

Parameters:

  • source (Union[pathlib.Path, str]) – SBML to annotation

  • annotations_path (pathlib.Path) – external file with annotations

  • filepath (pathlib.Path) – annotated SBML file

Returns:

annotated SBMLDocument

Return type:

libsbml.SBMLDocument

sbmlutils.metadata.annotator.annotate_sbml_doc(doc, external_annotations)[source]

Annotates given SBML document using the annotations file.

Parameters:

  • doc (libsbml.SBMLDocument) – SBMLDocument

  • external_annotations (List[ExternalAnnotation]) – ModelAnnotations

Returns:

annotated SBMLDocument

Return type:

libsbml.SBMLDocument

class sbmlutils.metadata.annotator.ExternalAnnotation(d)[source]

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

Parameters:

d (Dict) –

_keys = ['pattern', 'sbml_type', 'annotation_type', 'qualifier', 'resource', 'name'][source]
_sbml_types[source]
_annotation_types[source]
static _parse_qualifier_str(qualifier)[source]
Parameters:

qualifier (Optional[str]) –

Return type:

Union[pymetadata.identifiers.miriam.BQB, pymetadata.identifiers.miriam.BQM]

check()[source]

Check for valid choices.

Raise:

ValueError

Return type:

None

__str__()[source]

Convert to string.

Return type:

str

class sbmlutils.metadata.annotator.ModelAnnotator(doc, annotations)[source]

Helper class for annotating SBML models.

Parameters:
annotate_model()[source]

Annotate the model with the given annotations.

Return type:

None

_get_ids_from_model()[source]

Create dictionary of ids for given model for lookup.

Returns:

Return type:

Dict[str, List[str]]

static _get_matching_ids(ids, pattern)[source]

Ids matching the regular expression.

Parameters:

  • ids (Iterable[str]) –

  • pattern (str) –

Return type:

List[str]

static _elements_from_ids(model, sbml_ids, sbml_type=None)[source]

Get list of SBML elements from given ids.

Parameters:

  • model (libsbml.Model) – SBML model

  • sbml_ids (Iterable[str]) – SBML SIds

  • sbml_type (Optional[str]) – type of SBML objects

Returns:

Return type:

List[libsbml.SBase]

_annotate_elements(elements, ex_a)[source]

Annotate given elements with annotation.

Parameters:

  • elements (Iterable[libsbml.SBase]) – SBase elements to annotate

  • ex_a (ExternalAnnotation) – annotation

Returns:

Return type:

None

static get_SBMLQualifier(qualifier_str, qualifier_type)[source]

Lookup of SBMLQualifier for given qualifier string.

Parameters:

  • qualifier_type (str) – BQB or BQM

  • qualifier_str (str) –

Returns:

SBML qualifier string

Return type:

str

static annotate_sbase(sbase, annotation)[source]

Annotate SBase based on given annotation data.

Parameters:

  • sbase (libsbml.SBase) – libsbml.SBase

  • annotation (pymetadata.core.annotation.RDFAnnotation) – Annotation

Returns:

Return type:

None

static read_annotations_df(file_path, file_format='*')[source]

Read annotations from given file into DataFrame.

Supports “xlsx”, “tsv”, “csv”, “json”, “*”

Parameters:

  • file_path (pathlib.Path) – either path to file, or data in dict format

  • file_format (str) – annotation file format

Returns:

pandas.DataFrame

Return type:

pandas.DataFrame

static read_annotations(file_path, file_format='*')[source]

Read annotations from given file into DataFrame.

Supports “xlsx”, “tsv”, “csv”, “json”, “*”

Parameters:

  • file_path (pathlib.Path) – either path to file, or data in dict format

  • file_format (str) – annotation file format

Returns:

list of annotation objects

Return type:

List[ExternalAnnotation]