Header

Frame

class fastobo.header.HeaderFrame(AbstractFrame)

append(object)

Append object to the end of the list.

Raises:

TypeError – when the object is not of the right type for this container (see type-level documentation for the required type).

clear()

Remove all items from list.

copy()

Return a shallow copy of the list.

count(value)

Return number of occurrences of value.

Raises:

TypeError – when the object is not of the right type for this container (see type-level documentation for the required type).

insert(index, object)

Insert object before index.

If index is greater than the number of elements in the list, object will be added at the end of the list.

pop(index=-1)

Remove and return item at index (default last).

Raises:

IndexError – when list is empty or index is out of range.

reverse()

Reverse IN PLACE.

Clauses

class fastobo.header.BaseHeaderClause(AbstractClause)

A header clause, appearing in the OBO header frame.

class fastobo.header.FormatVersionClause(BaseHeaderClause)

FormatVersionClause(version) –

A header clause indicating the format version of the OBO document.

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

version

the OBO format version used in document.

Type:

str

class fastobo.header.DataVersionClause(BaseHeaderClause)

DataVersionClause(version) –

A header clause indicating the version of the data in the OBO document.

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

version

the version of the data in the OBO document.

Type:

str

class fastobo.header.DateClause(BaseHeaderClause)

DateClause(date) –

A header clause indicating the date the document was last modified.

date

the date this document was last modified.

Type:

datetime

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.SavedByClause(BaseHeaderClause)

SavedByClause(name) –

A header clause containing the name of the person who saved the document.

name

the name of the person who saved the document.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.AutoGeneratedByClause(BaseHeaderClause)

AutoGeneratedByClause(name) –

A header clause indicating the software that generated the document.

name

the name of the software that generated the document.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.ImportClause(BaseHeaderClause)

ImportClause(reference) –

A clause with a URL or ontology ID referencing another OBO document.

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

reference

a reference to a document to import.

Type:

str

class fastobo.header.SubsetdefClause(BaseHeaderClause)

SubsetdefClause(subset, description) –

A header clause declaring a subset in the OBO document.

description

a description for the declared subset.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.SynonymTypedefClause(BaseHeaderClause)

SynonymTypedefClause(typedef, description, scope=None) –

A header clause declaring a synonym type in the OBO document.

description

the description of the declared synonym type.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

scope

the scope of the synonym type, or None.

Type:

str, optional

class fastobo.header.DefaultNamespaceClause(BaseHeaderClause)

DefaultNamespaceClause(namespace) –

A clause declaring the default namespace for the rest of the document.

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.IdspaceClause(BaseHeaderClause)

IdspaceClause(prefix, url, description=None) –

A clause giving the mapping between a “local” and a “global” ID space.

description

a description of this IDspace.

Type:

str, optional

prefix

the prefix used in prefixed IDs.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

url

the URL used to expand IDs of this IDspace.

Type:

Url

class fastobo.header.TreatXrefsAsEquivalentClause(BaseHeaderClause)

TreatXrefsAsEquivalentClause(idspace) –

A macro to treats xrefs coming from an ID space as equivalence statements.

idspace

the ID prefix to select some Xrefs with.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.TreatXrefsAsGenusDifferentiaClause(BaseHeaderClause)

TreatXrefsAsGenusDifferentiaClause(idspace, relation, filler) –

A macro to treats xrefs from an ID space as genus-differentia definitions.

idspace

the ID prefix to select some Xrefs with.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.TreatXrefsAsReverseGenusDifferentiaClause(BaseHeaderClause)

TreatXrefsAsReverseGenusDifferentiaClause(idspace, relation, filler) –

A macro to treats xrefs from an ID space as reverse genus-differentia definitions.

idspace

the ID prefix to select some Xrefs with.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.TreatXrefsAsRelationshipClause(BaseHeaderClause)

TreatXrefsAsRelationshipClause(idspace, relation) –

A macro to treats xrefs from an ID space as being relationships.

idspace

the ID prefix to select some Xrefs with.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.TreatXrefsAsIsAClause(BaseHeaderClause)

TreatXrefsAsIsAClause(idspace) –

A macro to treats xrefs from an ID space as being subclassing relations.

idspace

the ID prefix to select some Xrefs with.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.TreatXrefsAsHasSubclassClause(BaseHeaderClause)

TreatXrefsAsHasSubclassClause(idspace) –

A macro to treats xrefs from an ID space as being superclassing relations.

idspace

the ID prefix to select some Xrefs with.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.PropertyValueClause(BaseHeaderClause)

PropertyValueClause(property_value) –

A clause that binds a property to a value in the OBO document.

Parameters:

property_value (AbstractPropertyValue) – the property value to annotate the current OBO document with.

property_value

an annotation of the document.

Type:

AbstractPropertyValue

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.RemarkClause(BaseHeaderClause)

RemarkClause(remark) –

A header clause storing general comments for the current OBO file.

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

remark

a remark about the ontology.

Type:

str

class fastobo.header.OntologyClause(BaseHeaderClause)

OntologyClause(ontology) –

The ontology ID of the current OBO file.

ontology

the ID of the ontology described in the OBO document.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.OwlAxiomsClause(BaseHeaderClause)

OwlAxiomsClause(axioms) –

A header clause containing untranslatable OWL axioms.

axioms

raw OWL axioms that have no equivalent in the OBO language.

Type:

str

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

class fastobo.header.UnreservedClause(BaseHeaderClause)

UnreservedClause(tag, value) –

A tag/value pair not reserved in the OBO specification.

raw_tag()

Get the raw tag of the clause.

Returns:

str – the clause tag as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> clause = fastobo.header.OntologyClause("test")
>>> clause.raw_tag()
'ontology'
>>> str(clause)
'ontology: test'

raw_value()

Get the raw value of the clause.

Returns:

str – the clause value as it was extracted from the OBO header, stripped from trailing qualifiers and comment.

Example

>>> dt = datetime.datetime(2019, 4, 29, 21, 52)
>>> clause = fastobo.header.DateClause(dt)
>>> clause.date
datetime.datetime(2019, 4, 29, 21, 52)
>>> clause.raw_value()
'29:04:2019 21:52'

tag

The tag of the clause.

Type:

str

value

The value of the clause.

Type:

str