Document#

`OboDoc`#

class fastobo.doc.OboDoc(header=None, entities=None)#

–

The abstract syntax tree corresponding to an OBO document.

Parameters:

header (HeaderFrame, optional) – the header to use in the document. If None is given, an empty header is used instead.
entities (collections.abc.Iterable, optional) – an iterable of entity frames, either TermFrame, TypedefFrame or InstanceFrame.

__getitem__(key, /)#: Return self[key].

__len__()#: Return len(self).

__new__(**kwargs)#

__str__()#: Return str(self).

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.

compact_ids()#

Create a semantically equivalent OBO document with compact identifiers.

The OBO specification describes how to perform an URI decompaction using either ID spaces declared in the document header, builtin ID spaces, or a default rule using the purl.obolibrary.org domain. By applying the reverse operation, a new ontology can be created with compact identifiers. Some URLs may not have a compact representation if they don’t correspond to any decompaction rule.

Example

>>> doc = fastobo.loads(textwrap.dedent(
...     """
...     idspace: MassBank http://www.massbank.jp/jsp/FwdRecord.jsp?id=
...
...     [Term]
...     id: http://purl.obolibrary.org/obo/CHEBI_27958
...     xref: http://www.massbank.jp/jsp/FwdRecord.jsp?id=EA281701
...     """
... ))
>>> compact_doc = doc.compact_ids()
>>> print(compact_doc[0])
[Term]
id: CHEBI:27958
xref: MassBank:EA281701

See also

The Translation of Identifiers section of the OBO format version 1.4 specification.

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).

decompact_ids()#

Create a semantically equivalent OBO document with IRI identifiers.

The OBO specification describes how to perform an URI decompaction using either ID spaces declared in the document header, builtin ID spaces, or a default rule using the purl.obolibrary.org domain.

Example

>>> doc = fastobo.loads(textwrap.dedent(
...     """
...     idspace: MassBank http://www.massbank.jp/jsp/FwdRecord.jsp?id=
...
...     [Term]
...     id: CHEBI:27958
...     xref: MassBank:EA281701
...     """
... ))
>>> url_doc = doc.decompact_ids()
>>> print(url_doc[0])
[Term]
id: http://purl.obolibrary.org/obo/CHEBI_27958
xref: http://www.massbank.jp/jsp/FwdRecord.jsp?id=EA281701

Document#

OboDoc#

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`OboDoc`#