Python API¶

Data Model¶

The Python API client is primarily a GraphQL client that interacts with our GraphQL API endpoint. The data model for the python API client and the GraphQL API are identical.

If you prefer to query our API endpoint directly, it’s available at https://graphql.cryoetdataportal.cziscience.com/v1/graphql.

A simplified diagram of the graph data model is below:

API documentation¶

An API client library to facilitate use of the Cryo-Electron Tomography portal API. The Portal is a collection of high quality tomograms and metadata.

For more information on the API, visit the cryoet-data-portal repo: https://github.com/chanzuckerberg/cryoet-data-portal/

class cryoet_data_portal.Annotation¶

Metadata for an annotation

annotation_method¶

Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching)

Type:

str

annotation_publication¶

DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs.

Type:

str

annotation_software¶

Software used for generating this annotation

Type:

str

authors¶

The annotation authors of this annotation

Type:

List[AnnotationAuthor]

confidence_precision¶

Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive

Type:

float

confidence_recall¶

Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly

Type:

float

deposition¶

The deposition this annotation is a part of

Type:

Deposition

deposition_date¶

Date when an annotation set is initially received by the Data Portal.

Type:

date

deposition_id¶

If the annotation is part of a deposition, the related deposition’s id

Type:

int

files¶

The annotation files of this annotation

Type:

List[AnnotationFile]

ground_truth_status¶

Whether an annotation is considered ground truth, as determined by the annotator.

Type:

bool

ground_truth_used¶

Annotation filename used as ground truth for precision and recall

Type:

str

https_metadata_path¶

HTTPS path for the metadata json file for this annotation

Type:

str

id¶

Numeric identifier (May change!)

Type:

int

is_curator_recommended¶

Data curator’s subjective choice as the best annotation of the same annotation object ID

Type:

bool

last_modified_date¶

Date when an annotation was last modified in the Data Portal

Type:

date

method_type¶

The method type for generating the annotation (e.g. manual, hybrid, automated)

Type:

str

object_count¶

Number of objects identified

Type:

int

object_description¶

A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state.

Type:

str

object_id¶

Gene Ontology Cellular Component identifier for the annotation object

Type:

str

object_name¶

Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane)

Type:

str

object_state¶

Molecule state annotated (e.g. open, closed)

Type:

str

release_date¶

Date when annotation data is made public by the Data Portal.

Type:

date

s3_metadata_path¶

S3 path for the metadata json file for this annotation

Type:

str

tomogram_voxel_spacing¶

The tomogram voxel spacing this annotation is a part of

Type:

TomogramVoxelSpacing

tomogram_voxel_spacing_id¶

The ID of the tomogram voxel spacing this annotation is part of

Type:

int

download(dest_path=None, format=None, shape=None)¶

Download annotation files for a given format and/or shape

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

shape : Optional[str], optional¶

Choose a specific shape type to download (e.g.: OrientedPoint, SegmentationMask)

format : Optional[str], optional¶

Choose a specific file format to download (e.g.: mrc, ndjson)

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.AnnotationAuthor¶

Metadata for an annotation’s authors

affiliation_address¶

Address of the institution an annotator is affiliated with.

Type:

str

affiliation_identifier¶

A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).

Type:

str

affiliation_name¶

Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations.

Type:

str

annotation¶

The annotation this annotation author is a part of

Type:

Annotation

annotation_id¶

Reference to the annotation this author contributed to

Type:

int

author_list_order¶

The order in which the author appears in the publication

Type:

int

corresponding_author_status¶

Indicating whether an annotator is the corresponding author (YES or NO)

Type:

bool

email¶

Email address for this author

Type:

str

id¶

Numeric identifier for this annotation author (this may change!)

Type:

int

name¶

Full name of an annotation author (e.g. Jane Doe).

Type:

str

orcid¶

A unique, persistent identifier for researchers, provided by ORCID.

Type:

str

primary_annotator_status¶

Indicating whether an annotator is the main person executing the annotation, especially on manual annotation (YES or NO)

Type:

bool

primary_author_status¶

Indicating whether an author is the main person executing the annotation, especially on manual annotation (YES or NO)

Type:

bool

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.AnnotationFile¶

Metadata for an annotation file

annotation¶

The annotation this annotation file is a part of

Type:

Annotation

annotation_id¶

The ID of the annotation this file applies to

Type:

int

format¶

File format for this file

Type:

str

https_path¶

HTTPS path for this annotation file

Type:

str

id¶

Numeric identifier (May change!)

Type:

int

is_visualization_default¶

Data curator’s subjective choice of default annotation to display in visualization for an object

Type:

bool

s3_path¶

s3 path of the annotation file

Type:

str

shape_type¶

The type of the annotation

Type:

str

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Client¶

A GraphQL Client library that can traverse all the metadata in the CryoET Data Portal

Parameters:

url : Optional[str]

The API URL to connect to, defaults to the latest portal endpoint.

Returns:

A GraphQL API Client library

Examples

Generate a client that connects to the default GraphQL API:

>>> client = cryoet_data_portal.Client()

class cryoet_data_portal.Dataset¶

Metadata for a dataset

authors¶

The dataset authors of this dataset

Type:

List[DatasetAuthor]

cell_component_id¶

If the dataset focuses on a specific part of a cell, the subset is included here

Type:

str

cell_component_name¶

Name of the cellular component

Type:

str

cell_name¶

Name of the cell from which a biological sample used in a CryoET study is derived from.

Type:

str

cell_strain_id¶

Link to more information about the cell strain

Type:

str

cell_strain_name¶

Cell line or strain for the sample.

Type:

str

cell_type_id¶

Cell Ontology identifier for the cell type

Type:

str

dataset_citations¶

DOIs for publications that cite the dataset. Use a comma to separate multiple DOIs.

Type:

str

dataset_publications¶

DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs.

Type:

str

deposition¶

The deposition this dataset is a part of

Type:

Deposition

deposition_date¶

Date when a dataset is initially received by the Data Portal.

Type:

date

deposition_id¶

Reference to the deposition this dataset is associated with

Type:

int

description¶

A short description of a CryoET dataset, similar to an abstract for a journal article or dataset.

Type:

str

funding_sources¶

The dataset fundings of this dataset

Type:

List[DatasetFunding]

grid_preparation¶

Describe Cryo-ET grid preparation.

Type:

str

https_prefix¶

The https directory path where this dataset is contained

Type:

str

id¶

An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree

Type:

int

key_photo_thumbnail_url¶

URL for the thumbnail of preview image.

Type:

str

key_photo_url¶

URL for the dataset preview image.

Type:

str

last_modified_date¶

Date when a released dataset is last modified.

Type:

date

organism_name¶

Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens

Type:

str

organism_taxid¶

NCBI taxonomy identifier for the organism, e.g. 9606

Type:

str

other_setup¶

Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication

Type:

str

related_database_entries¶

If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers.

Type:

str

related_database_links¶

If a CryoET dataset is also deposited into another database, e.g. EMPIAR, enter the database identifier here (e.g.https://www.ebi.ac.uk/empiar/EMPIAR-12345/). Use a comma to separate multiple links.

Type:

str

release_date¶

Date when a dataset is made available on the Data Portal.

Type:

date

runs¶

The runs of this dataset

Type:

List[Run]

s3_prefix¶

The S3 public bucket path where this dataset is contained

Type:

str

sample_preparation¶

Describe how the sample was prepared.

Type:

str

sample_type¶

Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other)

Type:

str

tissue_id¶

UBERON identifier for the tissue

Type:

str

tissue_name¶

Name of the tissue from which a biological sample used in a CryoET study is derived from.

Type:

str

title¶

Title of a CryoET dataset

Type:

str

download_everything(dest_path=None)¶

Download all of the data for this dataset.

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DatasetAuthor¶

Metadata for authors of a dataset

affiliation_address¶

Address of the institution an author is affiliated with.

Type:

str

affiliation_identifier¶

A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).

Type:

str

affiliation_name¶

Name of the institutions an author is affiliated with. Comma separated

Type:

str

author_list_order¶

The order in which the author appears in the publication

Type:

int

corresponding_author_status¶

Indicating whether an author is the corresponding author

Type:

bool

dataset¶

The dataset this dataset author is a part of

Type:

Dataset

dataset_id¶

Numeric identifier for the dataset this author corresponds to

Type:

int

email¶

Email address for each author

Type:

str

id¶

A numeric identifier for this author (May change!)

Type:

int

name¶

Full name of a dataset author (e.g. Jane Doe).

Type:

str

orcid¶

A unique, persistent identifier for researchers, provided by ORCID.

Type:

str

primary_author_status¶

Indicating whether an author is the main person associated with the corresponding dataset

Type:

bool

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DatasetFunding¶

Metadata for a dataset’s funding sources

dataset¶

The dataset this dataset funding is a part of

Type:

Dataset

dataset_id¶

Numeric identifier for the dataset this funding source corresponds to

Type:

int

funding_agency_name¶

Name of the funding agency.

Type:

str

grant_id¶

Grant identifier provided by the funding agency.

Type:

str

id¶

A numeric identifier for this funding record (May change!)

Type:

int

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Deposition¶

Deposition metadata

annotations¶

The annotations of this deposition

Type:

List[Annotation]

authors¶

The deposition authors of this deposition

Type:

List[DepositionAuthor]

dataset¶

The datasets of this deposition

Type:

List[Dataset]

deposition_date¶

The date the deposition was deposited

Type:

date

deposition_publications¶

The publications related to this deposition

Type:

str

deposition_types¶

The types of data submitted as a part of this deposition

Type:

str

description¶

Description for the deposition

Type:

str

https_prefix¶

The https directory path where data about this deposition is contained

Type:

str

id¶

Numeric identifier for this depositions

Type:

int

key_photo_thumbnail_url¶

URL for the deposition thumbnail image.

Type:

str

key_photo_url¶

URL for the deposition preview image.

Type:

str

last_modified_date¶

The date the deposition was last modified

Type:

date

related_database_entries¶

The related database entries to this deposition

Type:

str

release_date¶

The date the deposition was released

Type:

date

s3_prefix¶

The S3 public bucket path where data about this deposition is contained

Type:

str

tiltseries¶

The tilt series of this deposition

Type:

List[TiltSeries]

title¶

Title for the deposition

Type:

str

tomograms¶

The tomograms of this deposition

Type:

List[Tomogram]

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.DepositionAuthor¶

Authors for a deposition

affiliation_address¶

Address of the institution an author is affiliated with.

Type:

str

affiliation_identifier¶

A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).

Type:

str

affiliation_name¶

Name of the institution an author is affiliated with.

Type:

str

author_list_order¶

The order in which the author appears in the publication

Type:

int

corresponding_author_status¶

Indicates whether an author is the corresponding author

Type:

bool

deposition¶

The deposition this deposition author is a part of

Type:

Deposition

deposition_id¶

Reference to the deposition this author contributed to

Type:

int

email¶

Email address for this author

Type:

str

id¶

Numeric identifier for this deposition author (this may change!)

Type:

int

name¶

Full name of a deposition author (e.g. Jane Doe).

Type:

str

orcid¶

A unique, persistent identifier for researchers, provided by ORCID.

Type:

str

primary_author_status¶

Indicates whether an author is the main person creating the deposition

Type:

bool

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Run¶

Metadata for an experiment run

dataset¶

The dataset this run is a part of

Type:

Dataset

dataset_id¶

Reference to the dataset this run is a part of

Type:

int

https_prefix¶

The HTTPS directory path where this dataset is contained

Type:

str

id¶

Numeric identifier (May change!)

Type:

int

name¶

Short name for this experiment run

Type:

str

s3_prefix¶

The S3 public bucket path where this dataset is contained

Type:

str

tiltseries¶

The tilt series of this run

Type:

List[TiltSeries]

tomogram_voxel_spacings¶

The tomogram voxel spacings of this run

Type:

List[TomogramVoxelSpacing]

download_everything(dest_path=None)¶

Download all of the data for this run.

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.TiltSeries¶

Metadata about how a tilt series was generated, and locations of output files

acceleration_voltage¶

Electron Microscope Accelerator voltage in volts

Type:

int

aligned_tiltseries_binning¶

Binning factor of the aligned tilt series

Type:

int

binning_from_frames¶

Describes the binning factor from frames to tilt series file

Type:

float

camera_manufacturer¶

Name of the camera manufacturer

Type:

str

camera_model¶

Camera model name

Type:

str

data_acquisition_software¶

Software used to collect data

Type:

str

deposition¶

The deposition this tilt series is a part of

Type:

Deposition

deposition_id¶

Reference to the deposition this tiltseries is associated with

Type:

int

frames_count¶

Number of frames associated to the tilt series

Type:

int

https_alignment_file¶

HTTPS path to the alignment file for this tiltseries

Type:

str

https_angle_list¶

HTTPS path to the angle list file for this tiltseries

Type:

str

https_collection_metadata¶

HTTPS path to the collection metadata file for this tiltseries

Type:

str

https_mrc_bin1¶

HTTPS path to this tiltseries in MRC format (no scaling)

Type:

str

https_omezarr_dir¶

HTTPS path to this tomogram in multiscale OME-Zarr format

Type:

str

id¶

Numeric identifier for this tilt series (this may change!)

Type:

int

is_aligned¶

Tilt series is aligned

Type:

bool

microscope_additional_info¶

Other microscope optical setup information, in addition to energy filter, phase plate and image corrector

Type:

str

microscope_energy_filter¶

Energy filter setup used

Type:

str

microscope_image_corrector¶

Image corrector setup

Type:

str

microscope_manufacturer¶

Name of the microscope manufacturer

Type:

str

microscope_model¶

Microscope model name

Type:

str

microscope_phase_plate¶

Phase plate configuration

Type:

str

pixel_spacing¶

Pixel spacing equal in both axes in angstroms

Type:

float

related_empiar_entry¶

If a tilt series is deposited into EMPIAR, the EMPIAR dataset identifier

Type:

str

run¶

The run this tilt series is a part of

Type:

Run

run_id¶

The ID of the experimental run this tilt series is part of

Type:

int

s3_alignment_file¶

S3 path to the alignment file for this tilt series

Type:

str

s3_angle_list¶

S3 path to the angle list file for this tilt series

Type:

str

s3_collection_metadata¶

S3 path to the collection metadata file for this tiltseries

Type:

str

s3_mrc_bin1¶

S3 path to this tiltseries in MRC format (no scaling)

Type:

str

s3_omezarr_dir¶

S3 path to this tomogram in multiscale OME-Zarr format

Type:

str

spherical_aberration_constant¶

Spherical Aberration Constant of the objective lens in millimeters

Type:

float

tilt_axis¶

Rotation angle in degrees

Type:

float

tilt_max¶

Maximal tilt angle in degrees

Type:

float

tilt_min¶

Minimal tilt angle in degrees

Type:

float

tilt_range¶

Total tilt range in degrees

Type:

float

tilt_series_quality¶

Author assessment of tilt series quality within the dataset (1-5, 5 is best)

Type:

int

tilt_step¶

Tilt step in degrees

Type:

float

tilting_scheme¶

The order of stage tilting during acquisition of the data

Type:

str

total_flux¶

Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series

Type:

float

download_alignment_file(dest_path=None)¶

Download the alignment file for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_angle_list(dest_path=None)¶

Download the angle list for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_collection_metadata(dest_path=None)¶

Download the collection metadata for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_mrcfile(dest_path=None)¶

Download an MRC file for this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_omezarr(dest_path=None)¶

Download the omezarr version of this tiltseries

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.Tomogram¶

Metadata for a tomogram

affine_transformation_matrix¶

The flip or rotation transformation of this author submitted tomogram is indicated here

Type:

str

authors¶

The tomogram authors of this tomogram

Type:

List[TomogramAuthor]

ctf_corrected¶

Whether this tomogram is CTF corrected

Type:

bool

deposition¶

The deposition this tomogram is a part of

Type:

Deposition

deposition_id¶

If the tomogram is part of a deposition, the related deposition’s id

Type:

int

fiducial_alignment_status¶

Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial

Type:

str

https_mrc_scale0¶

HTTPS path to this tomogram in MRC format (no scaling)

Type:

str

https_omezarr_dir¶

HTTPS path to this tomogram in multiscale OME-Zarr format

Type:

str

id¶

Numeric identifier for this tomogram (this may change!)

Type:

int

is_canonical¶

Is this tomogram considered the canonical tomogram for the run experiment? True=Yes

Type:

bool

key_photo_thumbnail_url¶

URL for the thumbnail of key photo

Type:

str

key_photo_url¶

URL for the key photo

Type:

str

name¶

Short name for this tomogram

Type:

str

neuroglancer_config¶

the compact json of neuroglancer config

Type:

str

offset_x¶

x offset data relative to the canonical tomogram in pixels

Type:

int

offset_y¶

y offset data relative to the canonical tomogram in pixels

Type:

int

offset_z¶

z offset data relative to the canonical tomogram in pixels

Type:

int

processing¶

Describe additional processing used to derive the tomogram

Type:

str

processing_software¶

Processing software used to derive the tomogram

Type:

str

reconstruction_method¶

Describe reconstruction method (Weighted back-projection, SART, SIRT)

Type:

str

reconstruction_software¶

Name of software used for reconstruction

Type:

str

s3_mrc_scale0¶

S3 path to this tomogram in MRC format (no scaling)

Type:

str

s3_omezarr_dir¶

S3 path to this tomogram in multiscale OME-Zarr format

Type:

str

scale0_dimensions¶

comma separated x,y,z dimensions of the unscaled tomogram

Type:

str

scale1_dimensions¶

comma separated x,y,z dimensions of the scale1 tomogram

Type:

str

scale2_dimensions¶

comma separated x,y,z dimensions of the scale2 tomogram

Type:

str

size_x¶

Number of pixels in the 3D data fast axis

Type:

int

size_y¶

Number of pixels in the 3D data medium axis

Type:

int

size_z¶

Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt

Type:

int

tomogram_version¶

Version of tomogram using the same software and post-processing. Version of tomogram using the same software and post-processing. This will be presented as the latest version

Type:

str

tomogram_voxel_spacing¶

The tomogram voxel spacing this tomogram is a part of

Type:

TomogramVoxelSpacing

tomogram_voxel_spacing_id¶

The ID of the tomogram voxel spacing this tomogram is part of

Type:

int

type¶

Tomogram purpose (ex: CANONICAL)

Type:

str

voxel_spacing¶

Voxel spacing equal in all three axes in angstroms

Type:

float

download_all_annotations(dest_path=None, format=None, shape=None)¶

Download all annotation files for this tomogram

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

shape : Optional[str], optional¶

Choose a specific shape type to download (e.g.: OrientedPoint, SegmentationMask)

format : Optional[str], optional¶

Choose a specific file format to download (e.g.: mrc, ndjson)

download_mrcfile(dest_path=None)¶

Download an MRC file of this tomogram

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

download_omezarr(dest_path=None)¶

Download the OME-Zarr version of this tomogram

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.TomogramAuthor¶

Metadata for a tomogram’s authors

affiliation_address¶

Address of the institution an author is affiliated with.

Type:

str

affiliation_identifier¶

A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR).

Type:

str

affiliation_name¶

Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations.

Type:

str

author_list_order¶

The order in which the author appears in the publication

Type:

int

corresponding_author_status¶

Indicating whether an author is the corresponding author (YES or NO)

Type:

bool

email¶

Email address for this author

Type:

str

id¶

Numeric identifier for this tomogram author (this may change!)

Type:

int

name¶

Full name of an author (e.g. Jane Doe).

Type:

str

orcid¶

A unique, persistent identifier for researchers, provided by ORCID.

Type:

str

primary_author_status¶

Indicating whether an author is the main person creating the tomogram (YES or NO)

Type:

bool

tomogram¶

The tomogram this tomogram author is a part of

Type:

Tomogram

tomogram_id¶

Reference to the tomogram this author contributed to

Type:

int

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes

class cryoet_data_portal.TomogramVoxelSpacing¶

Metadata for a given voxel spacing related to tomograms and annotations

annotations¶

The annotations of this tomogram voxel spacing

Type:

List[Annotation]

https_prefix¶

The HTTPS directory path where this tomogram voxel spacing is contained

Type:

str

id¶

Numeric identifier (May change!)

Type:

int

run¶

The run this tomogram voxel spacing is a part of

Type:

Run

run_id¶

The ID of the run this tomogram voxel spacing is a part of

Type:

int

s3_prefix¶

The S3 public bucket path where this tomogram voxel spacing is contained

Type:

str

tomograms¶

The tomograms of this tomogram voxel spacing

Type:

List[Tomogram]

voxel_spacing¶

The voxel spacing for the tomograms in this set in angstroms

Type:

float

download_everything(dest_path=None)¶

Download all of the data for this tomogram voxel spacing.

Parameters:

dest_path : Optional[str], optional¶

Choose a destination directory. Defaults to $CWD.

classmethod find(client, query_filters=None)¶

Find objects based on a set of search filters.

Search filters are combined with and so all results will match all filters.

Expressions with python-native operators (==, !=, >, >=, <, <=) must be in the format:

ModelSubclass.field {operator} {value}

Example:

• Tomogram.voxel_spacing.run.name == "RUN1"

Expressions with method operators (like, ilike, _in) must be in the format:

ModelSubclass.field.{operator}({value})

Examples:

• Tomogram.voxel_spacing.run.name.like("%RUN1%")

• Tomogram.voxel_spacing.run.name._in(["RUN1", "RUN2"])

Supported operators are: ==, !=, >, >=, <, <=, like, ilike, _in

• like is a partial match, with the % character being a wildcard

• ilike is similar to like but case-insensitive

• _in accepts a list of values that are acceptable matches.

Values may be strings or numbers depending on the type of the field being matched, and _in supports a list of values of the field’s corresponding type.

ModelSubclass.field may be an arbitrarily nested path to any field on any related model, such as:

ModelSubclass.related_class_field.related_field.second_related_class_field.second_field

Parameters:

client¶

A CryoET Portal API Client

query_filters=None¶

A set of expressions that narrow down the search results

Yields:

Matching Model objects.

Examples

Filter runs by attributes, including attributes in related models:

>>> runs = Run.find(client, query_filters=[Run.name == "TS_026", Run.dataset.id == 10000])
>>> runs = Run.find(client, query_filters=[Run.name._in(['TS_026', 'TS_027']), Run.tomogram_voxel_spacings.annotations.object_name.ilike('%membrane%')])

Get all results for this type:

>>> runs = Run.find(client)

classmethod get_by_id(client, id)¶

Find objects by primary key

Parameters:

client¶

A CryoET Portal API Client

id¶

Unique identifier for the object

Returns:

A matching Model object if found, None otherwise.

Examples

Get a Run by ID:

>>> run = Run.get_by_id(client, 1)
    print(run.name)

to_dict()¶

Return a dictionary representation of this object’s attributes