Models 

Class models for storing and representing ISA data, with particular focus on ISA-Tab compatibility. The modeling follows the structure of the specifications with different classes for each file type (investigation, study, assay), investigation sections, the different study and assay column types etc. In particular, study and assay data (i.e. corresponding materials and processes) are represented by use of directed acyclic graphs.

Note that all models are immutable after construction. Here is a common pattern for getting a copy with modifying select members.

>>> import attr
>>> from altamisa.isatab import Comment
>>> c1 = Comment(name="Name", value="the value")
>>> c1
Comment(name='Name', value='value')
>>> c2 = Comment(**{**attr.asdict(c1), "name": "Another Name"})
>>> c2
Comment(name='Another Name', value='value')

altamisa.isatab.AnnotatedStr 

class altamisa.isatab.AnnotatedStr(value, *args, **kwargs)[source]

A str that can be flagged with values.

Example Usage

>>> x = AnnotateStr("text", key1="value1", key2=2)
>>> x
"text"
>>> x.key1
"value1"
>>> x.key2
2

altamisa.isatab.OntologyTermRef 

class altamisa.isatab.OntologyTermRef(name: str = None, accession: str = None, ontology_name: str = None)[source]

Reference to a term into an ontology.

Can be either initialized with

all three of a name, an accession, and an ontology_name
only a name
nothing (empty)

name: str: Human-readable name of the term

accession: str: The accession of the referenced term

ontology_name: str: Name of the ontology (links to OntologyRef.name)

altamisa.isatab.Comment 

class altamisa.isatab.Comment(name: str, value: str)[source]

Representation of a Comment[*] cell.

name: str: Comment name

value: str: Comment value

altamisa.isatab.OntologyRef 

class altamisa.isatab.OntologyRef(name: str, file: str, version: str, description: str, comments: Tuple[Comment], headers: List[str])[source]

Description of an ontology term source, as used for investigation file.

name: str: The name of the ontology (e.g., CEBI)

file: str: Path to file or URI to ontology

version: str: Version of the ontology

description: str: Description of the ontology

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.BasicInfo 

class altamisa.isatab.BasicInfo(path: Path, identifier: str, title: str, description: str, submission_date: date, public_release_date: date, comments: Tuple[Comment], headers: List[str])[source]

Basic metadata for an investigation or study (INVESTIGATION or STUDY).

path: Path: Path to the investigation or study file

identifier: str: Investigation/Study identifier

title: str: Investigation/Study title

description: str: Investigation/Study description

submission_date: date: Investigation/Study submission date

public_release_date: date: Investigation/Study public release date

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.PublicationInfo 

class altamisa.isatab.PublicationInfo(pubmed_id: str, doi: str, authors: str, title: str, status: OntologyTermRef | str, comments: Tuple[Comment], headers: List[str])[source]

Information regarding an investigation publication (INVESTIGATION PUBLICATIONS).

pubmed_id: str: Publication PubMed ID

doi: str: Publication DOI

authors: str: Publication author list string

title: str: Publication title

status: OntologyTermRef | str: Publication status

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.ContactInfo 

class altamisa.isatab.ContactInfo(last_name: str, first_name: str, mid_initial: str, email: str, phone: str, fax: str, address: str, affiliation: str, role: OntologyTermRef | str, comments: Tuple[Comment], headers: List[str])[source]

Investigation contact information

last_name: str: Last name of contact

first_name: str: First name of contact

mid_initial: str: Middle initial of contact

email: str: Email of contact

phone: str: Phone of contact

fax: str: Fax no. of contact

address: str: Address of contact

affiliation: str: Affiliation of contact

role: OntologyTermRef | str: Role of contact

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.DesignDescriptorsInfo 

class altamisa.isatab.DesignDescriptorsInfo(type: OntologyTermRef | str, comments: Tuple[Comment], headers: List[str])[source]

Study design descriptors information

type: OntologyTermRef | str: Design descriptors type

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.FactorInfo 

class altamisa.isatab.FactorInfo(name: str, type: OntologyTermRef | str, comments: Tuple[Comment], headers: List[str])[source]

Study factor information

name: str: Factor name

type: OntologyTermRef | str: Factor type

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.AssayInfo 

class altamisa.isatab.AssayInfo(measurement_type: OntologyTermRef | str, technology_type: OntologyTermRef | str, platform: str, path: Path, comments: Tuple[Comment], headers: List[str])[source]

Study assay information

measurement_type: OntologyTermRef | str: Assay measurement type

technology_type: OntologyTermRef | str: Assay technology type

platform: str: Assay platform

path: Path: Path to assay file

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.ProtocolComponentInfo 

class altamisa.isatab.ProtocolComponentInfo(name: str, type: OntologyTermRef | str)[source]

Protocol component information

name: str: Protocol component name

type: OntologyTermRef | str: Protocol component type

altamisa.isatab.ProtocolInfo 

class altamisa.isatab.ProtocolInfo(name: str, type: OntologyTermRef | str, description: str, uri: str, version: str, parameters: Dict[str, OntologyTermRef | str], components: Dict[str, ProtocolComponentInfo], comments: Tuple[Comment], headers: List[str])[source]

Protocol information

name: str: Protocol name

type: OntologyTermRef | str: Protocol type

description: str: Protocol

uri: str: Protocol URI

version: str: Protocol version

parameters: Dict[str, OntologyTermRef | str]: Protocol parameters

components: Dict[str, ProtocolComponentInfo]: Protocol components

comments: Tuple[Comment]: Comments

headers: List[str]: Headers from/for ISA-tab parsing/writing

altamisa.isatab.StudyInfo 

class altamisa.isatab.StudyInfo(info: BasicInfo, designs: Tuple[DesignDescriptorsInfo], publications: Tuple[PublicationInfo], factors: Dict[str, FactorInfo], assays: Tuple[AssayInfo], protocols: Dict[str, ProtocolInfo], contacts: Tuple[ContactInfo])[source]

The full metadata regarding one study

info: BasicInfo: Basic study information

designs: Tuple[DesignDescriptorsInfo]: Study designs by name

publications: Tuple[PublicationInfo]: Publication list for study

factors: Dict[str, FactorInfo]: Study factors by name

assays: Tuple[AssayInfo]: Study assays

protocols: Dict[str, ProtocolInfo]: Study protocols by name

contacts: Tuple[ContactInfo]: Study contact list

altamisa.isatab.InvestigationInfo 

class altamisa.isatab.InvestigationInfo(ontology_source_refs: Dict[str, OntologyRef], info: BasicInfo, publications: Tuple[PublicationInfo], contacts: Tuple[ContactInfo], studies: Tuple[StudyInfo])[source]

Representation of an ISA investigation

ontology_source_refs: Dict[str, OntologyRef]: Ontologies defined for investigation

info: BasicInfo: Basic information on investigation

publications: Tuple[PublicationInfo]: List of investigation publications

contacts: Tuple[ContactInfo]: Contact list for investigation

studies: Tuple[StudyInfo]: List of studies in this investigation

altamisa.isatab.Characteristics 

class altamisa.isatab.Characteristics(name: str, value: List[OntologyTermRef | str], unit: OntologyTermRef | str)[source]

Representation of a Characteristics[*] cell.

name: str: Characteristics name

value: List[OntologyTermRef | str]: Characteristics value

unit: OntologyTermRef | str: Characteristics unit

altamisa.isatab.FactorValue 

class altamisa.isatab.FactorValue(name: str, value: OntologyTermRef | str, unit: OntologyTermRef | str)[source]

Representation of a Factor Value[*] cell.

name: str: Factor name

value: OntologyTermRef | str: Factor value

unit: OntologyTermRef | str: Factor value unit

altamisa.isatab.ParameterValue 

class altamisa.isatab.ParameterValue(name: str, value: List[OntologyTermRef | str], unit: OntologyTermRef | str)[source]

Representation of a Parameter Value[*] cell.

name: str: Parameter name

value: List[OntologyTermRef | str]: Parameter value

unit: OntologyTermRef | str: Parameter value unit

altamisa.isatab.Material 

class altamisa.isatab.Material(type: str, unique_name: str, name: str, extract_label: OntologyTermRef | str, characteristics: Tuple[Characteristics], comments: Tuple[Comment], factor_values: Tuple[FactorValue], material_type: OntologyTermRef | str, headers: List[str])[source]

Representation of a Material or Data node.

type: str: The type of node (i.e. column name)

unique_name: str: The unique name of the material node. This is usually created with respect to study/assay and column. The unique name is necessary to distinguish materials of different type with potential overlaps in names. Otherwise graph representation might be incorrect (ambiguous arcs, loops) and the original relation of material and process not conclusively reproducible.

name: str: Original name of a material or data file

extract_label: OntologyTermRef | str: The label of a Labeled Extract

characteristics: Tuple[Characteristics]: Material characteristics

comments: Tuple[Comment]: Material comments

factor_values: Tuple[FactorValue]: Material factor values

material_type: OntologyTermRef | str: Material type

headers: List[str]: Columns headers from/for ISA-tab parsing/writing

altamisa.isatab.Process 

class altamisa.isatab.Process(protocol_ref: str, unique_name: str, name: str, name_type: str, date: date, performer: str, parameter_values: Tuple[ParameterValue], comments: Tuple[Comment], array_design_ref: str, first_dimension: OntologyTermRef | str, second_dimension: OntologyTermRef | str, headers: List[str])[source]

Representation of a Process or Assay node.

protocol_ref: str: Referenced to protocol name from investigation

unique_name: str: The unique name of the process node. This is usually created with respect to study/assay and column. The unique name is necessary to distinguish processes of different protocols with potential overlaps in names. Otherwise graph representation might be incorrect (ambiguous arcs, loops) and the original relation of material and process not conclusively reproducible. When “Protocol REF” is given without a further qualifying name, this is generated from the protocol reference with an auto-incrementing number.

name: str: Original name of a process (e.g. from Assay Name etc.)

name_type: str: Type of original name (e.g. Assay Name)

date: date: Process date

performer: str: Performer of process

parameter_values: Tuple[ParameterValue]: Tuple of parameters values

comments: Tuple[Comment]: Tuple of process comments

array_design_ref: str

Array design reference (special case annotation)

Technology types: “DNA microarray”, “protein microarray”

Protocol types: “nucleic acid hybridization”, “hybridization”

first_dimension: OntologyTermRef | str

First dimension (special case annotation, INSTEAD of Gel Electrophoresis Assay Name)

Technology types: “gel electrophoresis”

Protocol types: “electrophoresis”

second_dimension: OntologyTermRef | str

Second dimension (special case annotation, INSTEAD of Gel Electrophoresis Assay Name)

Technology types: “gel electrophoresis”

Protocol types: “electrophoresis”

headers: List[str]: Columns headers from/for ISA-tab parsing/writing

altamisa.isatab.Arc 

class altamisa.isatab.Arc(tail: str, head: str)[source]

Representation of an arc between two Material and/or Process nodes.

tail: str: The arc’s tail name

head: str: The arc’s head name

altamisa.isatab.Study 

class altamisa.isatab.Study(file: Path, header: Tuple, materials: Dict[str, Material], processes: Dict[str, Process], arcs: Tuple[Arc])[source]

Representation of an ISA study.

file: Path: Path to ISA study file

header: Tuple: The study’s header

materials: Dict[str, Material]: A mapping from material name to Material object (Data is a kind of material)

processes: Dict[str, Process]: A mapping from process name to Process object

arcs: Tuple[Arc]: The processing arcs

altamisa.isatab.Assay 

class altamisa.isatab.Assay(file: Path, header: Tuple, materials: Dict[str, Material], processes: Dict[str, Process], arcs: Tuple[Arc])[source]

Representation of an ISA assay.

file: Path: Path to ISA assay file

header: Tuple: The assay’s header

materials: Dict[str, Material]: A mapping from material name to Material object (Data is a kind of material)

processes: Dict[str, Process]: A mapping from process name to Process object

arcs: Tuple[Arc]: The processing arcs