curate_gpt.wrappers.bio package

Submodules

curate_gpt.wrappers.bio.alliance_gene_wrapper module

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class curate_gpt.wrappers.bio.alliance_gene_wrapper.AllianceGeneWrapper(source_locator=None, local_store=None, extractor=None, _label_adapter=None, taxon_id='NCBITaxon:9606')

Bases: BaseWrapper

A wrapper over a Alliance (AGR) gene API.

In future this may be extended to other objects.

default_object_type = 'Gene'
name: ClassVar[str] = 'alliance_gene'
object_ids(taxon_id=None, **kwargs)

Get all gene ids for a given taxon id

Parameters:

  • taxon_id (Optional[str])

  • kwargs

Return type:

Iterator[str]

Returns:

objects(collection=None, object_ids=None, **kwargs)

All genes

Parameters:

  • collection (Optional[str])

  • object_ids (Optional[Iterable[str]])

  • kwargs

Return type:

Iterator[Dict]

Returns:

taxon_id: str = 'NCBITaxon:9606'

curate_gpt.wrappers.bio.bacdive_wrapper module

Wrapper for JSON (or YAML) documents.

class curate_gpt.wrappers.bio.bacdive_wrapper.BacDiveWrapper(source_locator=None, local_store=None, extractor=None, format=None, path_expression=None)

Bases: BaseWrapper

A wrapper over a bacdive json files.

This is a static wrapper: it cannot be searched

default_object_type = 'OrganismTaxon'
format: str = None
name: ClassVar[str] = 'bacdive'
objects(collection=None, object_ids=None, **kwargs)

Return all objects in the view.

Parameters:

  • collection (Optional[str])

  • object_ids (Optional[Iterable[str]]) – Optional list of IDs to fetch

  • kwargs

Return type:

Iterator[Dict]

Returns:

path_expression: str = None
prefix: ClassVar[str] = 'bacdive'
wrap_object(obj)

Convert an object from the source representation to the store representation.

Parameters:

obj (Dict)

Return type:

Iterator[Dict]

Returns:

curate_gpt.wrappers.bio.gocam_wrapper module

class curate_gpt.wrappers.bio.gocam_wrapper.GOCAMWrapper(source_locator=None, local_store=None, extractor=None, _label_adapter=None, pubmed_wrapper=None, ro_adapter=None, session=<factory>, include_standard_annotations=False, **_kwargs)

Bases: BaseWrapper

An view over a GO CAM source.

default_object_type = 'Pathway'
include_standard_annotations: bool = False
property label_adapter: BasicOntologyInterface

Get the label adapter.

name: ClassVar[str] = 'gocam'
object_by_id(object_id)
Return type:

Optional[Dict]

object_from_dict(obj)
Return type:

Optional[Dict]

objects(collection=None, object_ids=None, **kwargs)

Return all objects in the view.

Parameters:

  • collection (Optional[str])

  • object_ids (Optional[Iterable[str]]) – Optional list of IDs to fetch

  • kwargs

Return type:

Iterator[Dict]

Returns:

pubmed_wrapper: PubmedWrapper = None
ro_adapter: BasicOntologyInterface = None
session: Session

curate_gpt.wrappers.bio.mediadive_wrapper module

class curate_gpt.wrappers.bio.mediadive_wrapper.MediaDiveWrapper(source_locator=None, local_store=None, extractor=None, _label_adapter=None)

Bases: BaseWrapper

A wrapper over MediaDive.

default_object_type = 'ComplexMixture'
name: ClassVar[str] = 'mediadive'
object_ids(**kwargs)

Get all medium ids in database

Parameters:

kwargs

Return type:

Iterator[str]

Returns:

objects(collection=None, object_ids=None, **kwargs)

All media

Parameters:

  • collection (Optional[str])

  • object_ids (Optional[Iterable[str]]) – optional list of object ids to retrieve (if None, all objects are retrieved)

  • kwargs

Return type:

Iterator[Dict]

Returns:

curate_gpt.wrappers.bio.omicsdi_wrapper module

Chat with a KB.

class curate_gpt.wrappers.bio.omicsdi_wrapper.OmicsDIWrapper(source_locator=None, local_store=None, extractor=None, source=None)

Bases: BaseWrapper

A wrapper to provide a search facade over OMICS DI Search.

This is a dynamic wrapper: it can be used as a search facade, but cannot be ingested in whole.

additional_info(local_id, source)

Augment the local ID with information from the database.

default_object_type = 'Dataset'

Search the OmicsDI database for the given text.

TODO: full text retrieval doesn’t seem to work well

Return type:

List[Dict]

name: ClassVar[str] = 'omicsdi'
objects_by_ids(ids, source=None)

Augment the local ID with information from the database.

source: str = None

curate_gpt.wrappers.bio.reactome_wrapper module

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class curate_gpt.wrappers.bio.reactome_wrapper.ReactomeWrapper(source_locator=None, local_store=None, extractor=None, _label_adapter=None, taxon_id='NCBITaxon:9606')

Bases: BaseWrapper

A wrapper over a Reactome API.

default_object_type = 'Event'
name: ClassVar[str] = 'reactome'
object_ids(taxon_id=None, **kwargs)

Get all object ids for a given taxon id

Parameters:

  • taxon_id (Optional[str])

  • kwargs

Return type:

Iterator[str]

Returns:

objects(collection=None, object_ids=None, **kwargs)

All events

Parameters:

  • collection (Optional[str])

  • object_ids (Optional[Iterable[str]])

  • kwargs

Return type:

Iterator[Dict]

Returns:

prefix: ClassVar[str] = 'Reactome'
taxon_id: str = 'NCBITaxon:9606'
curate_gpt.wrappers.bio.reactome_wrapper.generic_object(obj)
curate_gpt.wrappers.bio.reactome_wrapper.ids_from_tree(objs)

Recursively yield all ids from a tree of objects

Note: may contain duplicates

Parameters:

objs (List)

Returns:

curate_gpt.wrappers.bio.reactome_wrapper.pub_object(obj)
curate_gpt.wrappers.bio.reactome_wrapper.simple_entity_object(obj)
curate_gpt.wrappers.bio.reactome_wrapper.term_object(obj)

curate_gpt.wrappers.bio.uniprot_wrapper module

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class curate_gpt.wrappers.bio.uniprot_wrapper.UniprotWrapper(source_locator=None, local_store=None, extractor=None, _label_adapter=None, taxon_id=None, session=<factory>)

Bases: BaseWrapper

A wrapper over the UniProt API.

default_object_type = 'Protein'
name: ClassVar[str] = 'uniprot'
object_ids(taxon_id=None, **kwargs)

Get all gene ids for a given taxon id

Parameters:

  • taxon_id (Optional[str])

  • kwargs

Return type:

Iterator[str]

Returns:

objects(collection=None, object_ids=None, **kwargs)

All proteins

Return type:

Iterator[Dict]

objects_by_ids(object_ids)

Return objects by their IDs.

Parameters:

object_ids (List[str])

Return type:

List[Dict]

Returns:

session: CachedSession
taxon_id: Optional[str] = None

Module contents