\d*)
-serialize =
+serialize =
{major}.{minor}.{patch}{release}{num}
{major}.{minor}.{patch}
tag_name = {new_version}
@@ -15,7 +15,7 @@ tag_name = {new_version}
name = cobra
url = https://opencobra.github.io/cobrapy
download_url = https://pypi.org/project/cobra
-project_urls =
+project_urls =
Source Code = https://github.com/opencobra/cobrapy
Documentation = https://cobrapy.readthedocs.io
Bug Tracker = https://github.com/opencobra/cobrapy/issues
@@ -23,7 +23,7 @@ author = The cobrapy core development team.
author_email = cobra-pie@googlegroups.com
maintainer = Moritz E. Beber
maintainer_email = moritz.beber@gmail.com
-classifiers =
+classifiers =
Development Status :: 5 - Production/Stable
Intended Audience :: Science/Research
License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
@@ -41,7 +41,7 @@ license = LGPL-2.0-or-later OR GPL-2.0-or-later
description = COBRApy is a package for constraint-based modeling of metabolic networks.
long_description = file: README.rst, INSTALL.rst
long_description_content_type = text/x-rst
-keywords =
+keywords =
metabolism
biology
constraint-based
@@ -53,7 +53,7 @@ keywords =
[options]
zip_safe = True
-install_requires =
+install_requires =
appdirs ~=1.4
depinfo ~=1.7
diskcache ~=5.0
@@ -68,24 +68,25 @@ install_requires =
rich >=8.0
ruamel.yaml ~=0.16
swiglpk
-tests_require =
+ jsonschema
+tests_require =
tox
packages = find:
-package_dir =
+package_dir =
= src
[options.packages.find]
where = src
[options.package_data]
-cobra =
+cobra =
data/*
io/*.json
[options.extras_require]
-array =
+array =
scipy
-development =
+development =
black
bumpversion
isort
@@ -97,7 +98,7 @@ universal = 1
[bumpversion:part:release]
optional_value = placeholder
first_value = placeholder
-values =
+values =
placeholder
a
diff --git a/src/cobra/core/__init__.py b/src/cobra/core/__init__.py
index 12e082517..69379f9a5 100644
--- a/src/cobra/core/__init__.py
+++ b/src/cobra/core/__init__.py
@@ -1,10 +1,13 @@
from cobra.core.configuration import Configuration
from cobra.core.dictlist import DictList
-from cobra.core.gene import Gene, GPR
+from cobra.core.gene import GPR, Gene
+from cobra.core.group import Group
from cobra.core.metabolite import Metabolite
+from cobra.core.metadata import MetaData
+from cobra.core.metadata.cvterm import CVTerm, CVTermList, ExternalResources
+from cobra.core.metadata.history import Creator, History
from cobra.core.model import Model
from cobra.core.object import Object
from cobra.core.reaction import Reaction
-from cobra.core.group import Group
from cobra.core.solution import Solution, get_solution
from cobra.core.species import Species
diff --git a/src/cobra/core/group.py b/src/cobra/core/group.py
index 501a3ffc2..ac2e508b3 100644
--- a/src/cobra/core/group.py
+++ b/src/cobra/core/group.py
@@ -3,7 +3,6 @@
from typing import Iterable, Optional, Set
from warnings import warn
-from .dictlist import DictList
from .object import Object
diff --git a/src/cobra/core/metadata/__init__.py b/src/cobra/core/metadata/__init__.py
new file mode 100644
index 000000000..8bbb78957
--- /dev/null
+++ b/src/cobra/core/metadata/__init__.py
@@ -0,0 +1,7 @@
+"""Provide functions for loading, saving and modifying metadata annotations."""
+
+from cobra.core.metadata.cvterm import CVTerm, CVTermList, ExternalResources, Qualifier
+from cobra.core.metadata.helper import URL_IDENTIFIERS_PATTERN, parse_identifiers_uri
+from cobra.core.metadata.history import Creator, History
+from cobra.core.metadata.custompairs import KeyValuePairs
+from cobra.core.metadata.metadata import MetaData
diff --git a/src/cobra/core/metadata/custompairs.py b/src/cobra/core/metadata/custompairs.py
new file mode 100644
index 000000000..22e61b28d
--- /dev/null
+++ b/src/cobra/core/metadata/custompairs.py
@@ -0,0 +1,172 @@
+"""Class to deal with Key-Value pairs.
+
+Key-Value pairs are described in SBML FBC3. For the FBC3 standard, see
+https://github.com/bgoli/sbml-fbc-spec/blob/main/sf_svn/spec/main.pdf
+"""
+import uuid
+from collections import UserDict
+from typing import Dict, Iterable, Optional, Union
+from dataclasses import dataclass, field, fields, asdict
+
+from ...util import format_long_string
+
+
+@dataclass
+class KeyValueEntry:
+ """Single key-value entry.
+
+ The key is an attribute on the entry.
+
+ Parameters
+ ----------
+ key: str
+ Defined as mandatory in the FBC3 standard.
+ id: str
+ optional. Default None.
+ name: str
+ optional. Default None.
+ value: str
+ optional. Default None.
+ uri: str
+ Can be a URN or URL. Optional (default None).
+ """
+ key: str
+ id: Optional[str] = None
+ name: Optional[str] = None
+ value: Optional[str] = None
+ uri: Optional[str] = None
+
+ @staticmethod
+ def from_data(data: Optional[Union[Dict, "KeyValueEntry"]]) -> "KeyValueEntry":
+ """Make a KeyValueDict object using the data passed.
+
+ Parameters
+ ----------
+ data - dict or KeyValueEntry
+ If dict, will use the values of the dictionary to populate a new
+ KeyValueEntry. If None, will return empty KeyValueEntry.
+
+ Returns
+ -------
+ KeyValueEntry
+ """
+ if isinstance(data, KeyValueEntry):
+ return data
+ elif isinstance(data, dict):
+ if 'key' not in data:
+ data['key'] = uuid.uuid4().hex
+ return KeyValueEntry(**data)
+ else:
+ raise TypeError(f"Invalid format for KeyValueEntry: '{data}'")
+
+ def __str__(self) -> str:
+ """Get string representation of the KeyValueEntry as dictionary.
+
+ Returns
+ -------
+ str
+ """
+ return str(asdict(self))
+
+ def __repr__(self) -> str:
+ """Get string representation, including module and class name.
+
+ Returns
+ -------
+ str
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}"
+ f"({repr(self.key)}, {repr(self.id)}, {repr(self.name)}, {repr(self.value)}"
+ f", {repr(self.uri)})"
+ )
+
+
+class KeyValuePairs(UserDict):
+ """A UserDict to store KeyValueEntries.
+
+ Parameters
+ ----------
+ entries : Iterable
+ an iterable containing entry information
+ """
+
+ def __init__(self, entries: Iterable[Union[Dict, KeyValueEntry]] = None):
+ """Initialize the KeyValuePairs dictionary class.
+
+ Parameters
+ ----------
+ entries: Iterable
+ An iterable of dictionaries or KeyValueEntry, which will be inputted to the
+ dictionary.
+ """
+ super().__init__()
+ if entries:
+ for item in entries:
+ entry = KeyValueEntry.from_data(item)
+ self.data[entry.key] = entry
+
+ def __setitem__(self, key: str, item: Union[Dict, KeyValueEntry]) -> None:
+ """Set item.
+
+ Parameters
+ ----------
+ key: str
+ item: dictionary or KeyValueEntry
+ """
+ entry = KeyValueEntry.from_data(item)
+ self.data[key] = entry
+
+ def __str__(self) -> str:
+ """Convert KeyValuePairs to str.
+
+ Parameters
+ ----------
+ self : KeyValuePairs
+ UserDict defining key value pairs
+
+ Returns
+ ------
+ string
+ a string representation of a dictionary
+ """
+ return str(self.to_dict())
+
+ def __repr__(self) -> str:
+ """Get string representation, including module and class name.
+
+ Returns
+ -------
+ str
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}"
+ f"({self.to_dict()!r})"
+ )
+
+ def _repr_html_(self) -> str:
+ """Get HTML representation.
+
+ Returns
+ -------
+ str
+ HTML formatted string
+ """
+ return f"""KeyValuePairs
{format_long_string(
+ self.__str__(), 100)}
"""
+
+ def to_dict(self) -> dict:
+ """Get dictionary representation.
+
+ Returns
+ -------
+ dict
+ keys are the keys, and each value is the KeyValueEntry represented as
+ a dict.
+ """
+ return {k: asdict(v) for k, v in self.data.items()}
+
+ #query
+
+ #add_key_value_pair
+ #delete_key_value_pair?? Maybe with query
diff --git a/src/cobra/core/metadata/cvterm.py b/src/cobra/core/metadata/cvterm.py
new file mode 100644
index 000000000..726a5056a
--- /dev/null
+++ b/src/cobra/core/metadata/cvterm.py
@@ -0,0 +1,1148 @@
+"""Define the Controlled Vocabulary term class."""
+
+import re
+from collections import UserList
+from enum import Enum
+from typing import Callable, Dict, FrozenSet, Iterable, List, Optional, Pattern, Union
+
+from .helper import URL_IDENTIFIERS_PATTERN, parse_identifiers_uri
+
+
+class Qualifier(Enum):
+ """The possible qualifiers inside a CVTerm.
+
+ The qualifiers and their detailed description are present in
+ https://co.mbine.org/standards/qualifiers.
+
+ Qualifiers are divided into two groups
+ bqb These kinds of qualifiers define the relationship between a biological
+ object represented by a model element and its annotation.
+ bqm These kinds of qualifiers define the relationship between a modelling
+ object and its annotation.
+ """
+
+ bqb_is = "bqb_is"
+ bqb_hasPart = "bqb_hasPart"
+ bqb_isPartOf = "bqb_isPartOf"
+ bqb_isVersionOf = "bqb_isVersionOf"
+ bqb_hasVersion = "bqb_hasVersion"
+ bqb_isHomologTo = "bqb_isHomologTo"
+ bqb_isDescribedBy = "bqb_isDescribedBy"
+ bqb_isEncodedBy = "bqb_isEncodedBy"
+ bqb_encodes = "bqb_encodes"
+ bqb_occursIn = "bqb_occursIn"
+ bqb_hasProperty = "bqb_hasProperty"
+ bqb_isPropertyOf = "bqb_isPropertyOf"
+ bqb_hasTaxon = "bqb_hasTaxon"
+ bqb_unknown = "bqb_unknown"
+ bqm_is = "bqm_is"
+ bqm_isDescribedBy = "bqm_isDescribedBy"
+ bqm_isDerivedFrom = "bqm_isDerivedFrom"
+ bqm_isInstanceOf = "bqm_isInstanceOf"
+ bqm_hasInstance = "bqm_hasInstance"
+ bqm_unknown = "bqm_unknown"
+
+
+class CVTerm:
+ """CVTerm class, representing controlled vocabulary.
+
+ Controlled Vocabulary (CVTerm) can be defined as a curated and controlled
+ relationship, described by Qualifier (see above) - the relationship between an
+ object and annotation must be part of the Qualifier class. These relationships
+ are based in biochemical or biological relationships. The qualifiers/relationships
+ are divided into bqbiol/bqb (biological qualification) and bqmodel/bqm (model
+ qualifications). See two examples:
+ "bqb_is" The biological entity represented by the SBML component is the subject
+ of the referenced resource. This could serve to link a reaction to its counterpart
+ in (e.g.) the ChEBI or Reactome databases.
+ "bqm_is" The modeling object encoded by the SBML component is the subject of
+ the referenced resource. This might be used, e.g., to link the model
+ to an entry in a model database.
+ See https://co.mbine.org/standards/qualifiers
+ For a definition of all qualifiers, see SBML Level 3, Version 2 Core, p 104
+ (http://co.mbine.org/specifications/sbml.level-3.version-2.core.release-2.pdf)
+
+ The annotation will have one or more URI, which are encapsulated in
+ ExternalResources class (see below).
+
+ Each CVTerm has only ONE qualifier, and can have many URI in the resources. If
+ you need to use another qualifier, it can be nested data (if relevant), or it
+ should be in another CVTerm.
+ If an object has multiple CVTerms, they are placed in a CVTermList (see below).
+
+ This is how a CVTerm object looks :
+ CVTerm.qualifier = "bqb_is"
+ CVTerm.ex_res =
+ {"resources": [
+ "resource_uri",
+ ...
+ ],
+ "nested_data":CVTermList Object
+ }
+
+ Examples of how CVTerms can be used
+
+ Model examples (Each of these is a separate CVTerm)
+ qualifier=bqm_is
+ resources=["https://identifiers.org/biomodels.db/BIOMD0000000003"]
+ A model identifier
+ qualifier=bqm_isDescribed_by
+ resources=["https://identifiers.org/pubmed/1833774"]
+ A published article detailing the model
+ qualifier=bqm_isVersionOf
+ resources=["https://identifiers.org/wikipathways/WP179",
+ "https://identifiers.org/reactome/REACT_152"/]
+ Two links to what this model is a version of (in this case, cell cycle).
+
+ Reaction examples
+ qualifier=bqb_is
+ resources=["https://identifiers.org/reactome/REACT_6327"/]
+ A link to a reaction database that details reactions.
+ qualifier=bqb_hasPart
+ resources=["http://identifiers.org/uniprot/P04551",
+ http://identifiers.org/uniprot/P10815"]
+ resources.nested_date = {
+ qualifier=bqb_isDescribedby
+ resources=["https://identifiers.org/pubmed/1111111"]
+ Two proteins that form part of the same complex. The nested data links to an
+ article describing the formation of the complex.
+ It is nested data because it is relevant to the hasPart CVTerm, but uses a
+ different qualifier.
+ """
+
+ def __init__(
+ self,
+ ex_res: Optional[Union["ExternalResources", Dict, str]] = None,
+ qualifier: Union[Qualifier, str] = Qualifier.bqb_is,
+ ):
+ """Initialize a CVTerm.
+
+ Parameters
+ ----------
+ ex_res: ExternalResources or dict
+ The external resources (URI format), which may include nested data. Can be
+ qualifier: Qualifier or str
+ The qualifier for the relationship.
+ """
+ self._ex_res = None
+ self._qualifier = None
+ self._ex_res = self.check_ex_res_type(ex_res)
+ self._qualifier = self.check_qualifier_type(qualifier)
+
+ @property
+ def qualifier(self) -> Qualifier:
+ """Get qualifier for CVTerm.
+
+ Returns
+ -------
+ Qualifier
+ """
+ return self._qualifier
+
+ @qualifier.setter
+ def qualifier(self, qualifier: Union[str, Qualifier]) -> None:
+ """Set Qualifier.
+
+ Parameters
+ ----------
+ qualifier - str, int or Qualifier
+ Is converted to the Qualifier class.
+
+ See Also
+ --------
+ CVTerm.check_qualifier_type()
+ """
+ self._qualifier = self.check_qualifier_type(qualifier)
+
+ @property
+ def external_resources(self) -> "ExternalResources":
+ """Get external resources.
+
+ Returns
+ -------
+ ExternalResources
+ """
+ return self._ex_res
+
+ @external_resources.setter
+ def external_resources(
+ self, external_resources: Union[dict, "ExternalResources"]
+ ) -> None:
+ """Set external resources.
+
+ Parameters
+ ----------
+ external_resources - dict or ExternalResources
+ Is converted to the ExternalResources class.
+
+ See Also
+ --------
+ CVTerm.check_ex_res_type()
+ """
+ self._ex_res = self.check_ex_res_type(external_resources)
+
+ @property
+ def resources(self) -> FrozenSet:
+ """Get all resources.
+
+ Returns:
+ -------
+ FrozenSet:
+ a set of all resources in the CVTerm as a set of strings
+ including external resources of nested data as strings
+ """
+ return self.external_resources.resource_nested
+
+ @staticmethod
+ def check_ex_res_type(
+ ex_res: Optional[Union["ExternalResources", Dict, str]]
+ ) -> "ExternalResources":
+ """Check and parse input to ExternalResources.
+
+ Parameters
+ ----------
+ ex_res: ExternalResources or dict or str, optional
+ Input data to check if it is or can be transformed to ExternalResources
+ class. String must start with http:// or https:// to be acceptable.
+ Dictionary must match the format required by from_dict.
+ If None is given, an empty ExternalResources is returned.
+ No parsing of identifiers/URIs is done, perhaps in future versions.
+
+ Returns
+ -------
+ ExternalResources
+
+ Raises
+ ------
+ TypeError
+ If given anything other than None, str, dict or ExternalResources.
+ Will raise this error if given a string that does not start with http(s)://
+
+ See Also
+ --------
+ ExternalResources.from_dict()
+ """
+ if ex_res is None:
+ return ExternalResources()
+ elif isinstance(ex_res, ExternalResources):
+ return ex_res
+ elif isinstance(ex_res, dict):
+ return ExternalResources.from_dict(ex_res)
+ elif isinstance(ex_res, str) and ("http://" in ex_res or "https://" in ex_res):
+ return ExternalResources(resources=[ex_res])
+ else:
+ raise TypeError(
+ f"Allowed types for CVTerm ex_res are ExternalResources, str, None, "
+ f"or dict, not {type(ex_res)}: {ex_res}"
+ )
+
+ @staticmethod
+ def check_qualifier_type(qual: Union[str, Qualifier]) -> Qualifier:
+ """Check and parse input to Qualifier class.
+
+ Parameters
+ ----------
+ qual: str or Qualifier, optional
+ Input data to check if it is or can be transformed to Qualifier class.
+ Strings must be a member of the Qualifier values.
+ If None is given, an empty Qualifier is returned.
+
+ Returns
+ -------
+ Qualifier
+
+ Raises
+ ------
+ TypeError
+ If given anything other than None, str, or Qualifier.
+ Will raise this error if given a string that does not match the defined
+ Qualifier members.
+ """
+ if isinstance(qual, str) and qual not in Qualifier.__members__:
+ raise TypeError(f"{qual} is not a supported enum Qualifier")
+ elif isinstance(qual, Qualifier):
+ return qual
+ elif isinstance(qual, str):
+ return Qualifier[qual]
+ else:
+ raise TypeError(
+ f"Allowed types for CVTerm qualifier must be Qualifier,"
+ f"str member of the Qualifier enum {type(qual)}, {qual}"
+ )
+
+ def to_dict(self) -> Dict:
+ """Represent a CVTerm object in python dict.
+
+ Returns
+ -------
+ dict:
+ A dict that has two keys
+ "qualifier" - the qualifier as a string
+ "external_resources" - the resources as a dictionary
+
+ See Also
+ --------
+ ExternalResources.to_dict()
+
+ """
+ return {
+ "qualifier": self.qualifier.value,
+ "external_resources": self.external_resources.to_dict(),
+ }
+
+ @classmethod
+ def from_dict(cls, data_dict: Dict) -> "CVTerm":
+ """Generate a CVTerm object based on a python dict.
+
+ Parameters
+ ----------
+ data_dict: dict
+ A dict that has two keys
+ "qualifier" - the qualifier as a string, optional. If not present, the
+ qualifier is set to bqb_is.
+ "external_resources" - the resources as a dictionary, optional
+
+ Returns
+ -------
+ CVTerm
+
+ See Also
+ --------
+ ExternalResources.to_dict()
+
+ """
+ return cls(
+ ex_res=data_dict.get("external_resources", None),
+ qualifier=data_dict.get("qualifier", Qualifier["bqb_is"]),
+ )
+
+ def __eq__(self, other: Union["CVTerm", dict]) -> bool:
+ """Compare two CVTerm objects and return boolean for equality.
+
+ If a dict is given, it is transformed to CVTerm.
+ First, the qualifier is compared. If they are not identical, False is returned.
+ Then the external resources are compared, see ExternalResources.__eq__().
+
+ Parameters
+ ----------
+ other: dict or CVTerm
+
+ Returns
+ -------
+ bool
+ False if other is not CVTerm or dict.
+ False if qualifiers are different, or external resources are different.
+ True if qualifier and external resources are identical.
+
+ See Also
+ --------
+ CVTerm.from_dict()
+ ExternalResources.__eq__()
+ """
+ if not isinstance(other, (CVTerm, dict)):
+ return False
+ if isinstance(other, dict):
+ return self == CVTerm.from_dict(other)
+ if self.qualifier != other.qualifier:
+ return False
+ if self.external_resources != other.external_resources:
+ return False
+ return True
+
+ def __repr__(self) -> str:
+ """Return the CVTerm as str with module, class, and code to recreate it.
+
+ Returns
+ -------
+ str
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}"
+ f"({self.to_dict()})"
+ )
+
+ def _repr_html_(self) -> str:
+ """Return the CVTerm as HTML string with qualifier, resources and address.
+
+ Returns
+ -------
+ str
+ HTML formatted string
+ """
+ return f"""
+ {self.qualifier.name}:
+ "Resources"
+ {"
".join([res for res in self.external_resources.resources])}
+ Memory address{id(self):#x}
+ """
+
+
+class CVTermList(UserList):
+ """A list of CVTerm objects.
+
+ Representation of multiple CVTerm objects in a list. It is list that contains
+ CVTerm objects. As a list, it means that objects can repeat, and that the order is
+ maintained.
+
+ CVTermList is built using UserList, which means that the actual list can be
+ accessed using CVTermList.data. As a list, the order is kept, items may repeat.
+ __init__, __setitem__, __append__, __extend__ will check the data to make sure it
+ is a CVTerm or can be transformed to CVTerm using _check_CVTerm().
+ All list functions that are not overloaded will behave like standard lists.
+
+ Parameters
+ ----------
+ data : list
+ a list containing qualifier and external resources in CVTerm format
+
+ 1. The only way to add annotation data via old format is by
+ using the method "add_simple_annotations()". This will set all qualifiers as
+ "bqb_is". If you want to use other qualifiers and/or nested data, use
+ add_cvterms() or extend().
+ 2. Multiple CVTerm data can be added by using add_cvterms() or extend(). Both
+ accept iterables, including CVTermList.
+ """
+
+ def __init__(self, data: Iterable[Union[CVTerm, Dict]] = None):
+ """Initialize CVTermList object.
+
+ Parameters
+ ----------
+ data: Iterable of dict or CVTerm
+ Dicts will be transformed to CVTerm via _check_CVTerm.
+
+ Notes
+ -----
+ _check_CVTerm will raise TypeError if given a class other than dict or CVTerm,
+ so initialization of CVTermList may raise TypeError.
+ """
+ if data is None:
+ data = []
+ data = [self._check_CVTerm(datum) for datum in data]
+ super().__init__(data)
+
+ @staticmethod
+ def _check_CVTerm(cvterm: Union[CVTerm, Dict]) -> Optional["CVTerm"]:
+ if cvterm is None:
+ return
+ if isinstance(cvterm, CVTerm):
+ return cvterm
+ elif isinstance(cvterm, dict):
+ return CVTerm.from_dict(cvterm)
+ else:
+ raise TypeError(
+ f"Allowed types for CVTerm ex_res are CVTerm "
+ f"or dict, not {type(cvterm)}: {cvterm}"
+ )
+
+ @staticmethod
+ def from_data(data: Optional[Union[List, "CVTerm", "CVTermList"]]) -> "CVTermList":
+ """Parse a CVTermList object from given data.
+
+ Parameters
+ ----------
+ data: list, CVTerm or CVTermList or None, optional
+ This will be transformed to CVTermList class.
+ None will result in an empty CVTermList.
+ CVTerm will be placed in a list and become a CVTermList.
+ If given CVTermList, will return the data untransformed.
+
+ Returns
+ -------
+ CVTermList
+
+ Raises
+ ------
+ TypeError
+ If not given None, dict, CVTerm or CVTermList.
+ """
+ if data is None:
+ return CVTermList()
+ elif isinstance(data, list):
+ return CVTermList(data)
+ elif isinstance(data, CVTerm):
+ return CVTermList([data])
+ elif isinstance(data, CVTermList):
+ return data
+ else:
+ raise TypeError(f"Invalid format for CVTermList: '{data}'")
+
+ def to_list_of_dicts(self) -> List[dict]:
+ """Represent a CVTermList object as a list of python dicts.
+
+ Returns:
+ -------
+ list:
+ a list where each item is a dict, made by CVTerm.to_dict(). Used for JSON
+ and YAML export.
+
+ See Also
+ --------
+ CVTerm.to_dict()
+ """
+ return [cvterm.to_dict() for cvterm in self.data]
+
+ def add_cvterms(self, cvterms: Iterable[Union["CVTerm", Dict]]) -> None:
+ """Add multiple CVTerm to CVTermList.
+
+ Parameters
+ ----------
+ cvterms : Iterable
+ CVTermList list of CVTerms or CVTerm dicts to be added to the CVTermList
+ """
+ self.extend(cvterms)
+
+ def add_simple_annotations(self, data: Dict = None) -> None:
+ """Add simple annotation.
+
+ Adds standardized via old annotation format (dictionary like format).
+ The default qualifier, i.e "bqb_is", will be used.
+ This function will add identifiers.org to the keys given to form the URI.
+ If the annotation does not match the identifiers format, you should use
+ add_cvterms directly (and create the correct link) and/or use the
+ custompairs field of annotation.
+
+ This function will skip "sbo" keys since they should be added via
+ annotation["sbo"], see MetaData.
+
+ Parameters
+ ----------
+ data : dict
+ the data in old annotation format
+ keys are str representing namespace
+ If the value is a list, each value is added to the namespace, making a
+ CVTerm with one ExternalResources object htat has mulitple URIs. If the
+ value is a string, then only one value will be added to the namespace.
+
+ Examples
+ --------
+ >>> from cobra import Species
+ >>> s = Species()
+ >>> s.annotation.standardized.add_simple_annotations({"chebi": "CHEBI:17234"})
+ >>> s.annotation.standardized.add_simple_annotations({"chebi": ["CHBEI:1723456", "CHEBI:172345"]})
+ >>> s.annotation
+ >>> s.annotation.standardized
+ >>> s.annotation.annotations
+ """
+ if data is None:
+ data = {}
+
+ if not isinstance(data, dict):
+ raise TypeError(f"The data passed must be of type dict: {data}")
+
+ cvterm_list = []
+ for key, value in data.items():
+
+ if not isinstance(value, (list, str)):
+ raise TypeError(
+ f"The value passed must be of type list or str: {value}"
+ )
+ if key.lower() == "sbo":
+ continue
+
+ qual = Qualifier["bqb_is"]
+ # if there is only one identifier i.e. annotation
+ # of the form { "chebi": ["CHEBI:17234"]}
+ if isinstance(value, str):
+ uri = ["https://identifiers.org/" + key + "/" + value]
+ # if there are multiple identifiers for this key i.e. annotation
+ # of the form { "chebi": ["CHEBI:124", "CHEBI:17234"]}
+ elif isinstance(value, list):
+ uri = [
+ "https://identifiers.org/" + key + "/" + identifier
+ for identifier in value
+ ]
+ else:
+ raise TypeError(
+ f"The identifier passed must be of type string or list: {value}"
+ )
+ cvterm_list.append(CVTerm(ex_res=ExternalResources(uri), qualifier=qual))
+ self.add_cvterms(cvterm_list)
+
+ def delete_annotation(self, resource: Union[str, Pattern]) -> None:
+ """Delete annotation - the converse of add_simple_annotation.
+
+ This will go over the CVTerms, and delete all resources that match the pattern.
+ It will call the funciton recursively for ExternalResources that have
+ nested_data.
+ CVTerms that end with neither resources nor nested data are removed.
+
+ Parameters
+ ----------
+ resource: str or Pattern
+
+ Examples
+ --------
+ >>> from cobra.io import load_model
+ >>> e_coli = load_model('iJO1366')
+ >>> e_coli.annotation
+ >>> e_coli.annotation.standardized.delete_annotation('bigg')
+ >>> e_coli.annotation
+ >>> e_coli.annotation.annotations
+ >>> e_coli.metabolites[0].annotation.standardized
+ >>> e_coli.metabolites[0].annotation.standardized.delete_annotation(r'/bi\S+')
+ """
+ regex_searcher = re.compile(resource)
+ tmp_cvterm_list = []
+ for cvterm in self.data:
+ cvterm.external_resources.resources = [
+ res
+ for res in cvterm.external_resources.resources
+ if not regex_searcher.findall(res)
+ ]
+ if cvterm.external_resources.nested_data:
+ cvterm.external_resources.nested_data.delete_annotation(resource)
+ if (
+ cvterm.external_resources.resources
+ or cvterm.external_resources.nested_data
+ ):
+ tmp_cvterm_list.append(cvterm)
+ self.data = tmp_cvterm_list
+
+ @property
+ def annotations(self) -> Dict:
+ """Return CVTermList as annotation dictionary.
+
+ This function will return the CVTermList as a sorted annotation dictionary in
+ the older annotation format. In the dictionary, the keys are the namespaces,
+ while the values are lists of annotation identifiers.
+
+ Qualifiers are not present in the annotation dictionary. This function will
+ use CVTermList.resources(), which will get all resources of all CVTerm objects,
+ including nested resources.
+
+ Different CVTerms will be unified by namespace. Namespaces and values are
+ sorted in the dictionary, to avoid shifting caused by usage of sets.
+
+ For example, a CVTermList that looks like
+
+ [
+ {
+ "external_resources": {
+ "resources": [
+ "https://identifiers.org/uniprot/P69906",
+ "https://identifiers.org/uniprot/P68871",
+ "https://identifiers.org/kegg.compound/C00032",
+ ]
+ },
+ "qualifier": "bqb_hasPart",
+ },
+ {
+ "qualifier": "bqb_hasPart",
+ "external_resources": {
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://www.uniprot.org/uniprot/P68871",
+ "https://identifiers.org/chebi/CHEBI:17627",
+ ],
+ "nested_data": {
+ "qualifier": "bqb_isDescribedBy",
+ "external_resources": {
+ "resources": [
+ "https://identifiers.org/eco/000000",
+ ]
+ },
+ },
+ },
+ ]
+
+ Will be outputted as a dictionary that looks like
+ {
+ "chebi": ["CHEBI:17627"],
+ "eco": ["000000"],
+ "kegg.compound": ["C00032"],
+ "uniprot": ["P68871", "P69905", "P69906"],
+ }
+
+ Returns
+ -------
+ dict
+ Dictionary where keys are namespaces, sorted in ascending order. Values
+ are lists of identifiers, also sorted in ascentding order.
+
+ """
+ annotation_dict = {}
+ resources = self.resources
+ for res in resources:
+ if re.match(URL_IDENTIFIERS_PATTERN, res):
+ namespace, identifier = parse_identifiers_uri(res)
+ if namespace in annotation_dict.keys():
+ annotation_dict[namespace].append(identifier)
+ else:
+ annotation_dict[namespace] = [identifier]
+ return {k: sorted(annotation_dict[k]) for k in sorted(annotation_dict.keys())}
+
+ @property
+ def resources(self) -> FrozenSet[str]:
+ """Get all resources.
+
+ Returns:
+ -------
+ FrozenSet:
+ a set of all external resources in the original self.data list of CVTerms
+ including external resources of nested data. The Set contains the URIs as
+ strings, not in the ExternalResources format.
+ """
+ resources = set()
+ for datum in self.data:
+ if (
+ datum.external_resources.resources
+ or datum.external_resources.nested_data
+ ):
+ resources.update(datum.external_resources.resource_nested)
+ return frozenset(resources)
+
+ @property
+ def qualifiers(self) -> FrozenSet[Qualifier]:
+ """Get all qualifiers used by CVTerm objects in the CVTermList.
+
+ Returns:
+ -------
+ FrozenSet:
+ a frozen set of all qualifiers in the original self.data list of CVTerms
+ """
+ qualifier_set = set()
+ for datum in self.data:
+ qualifier_set.add(datum.qualifier)
+ return frozenset(qualifier_set)
+
+ def query(
+ self,
+ search_function: Union[str, Pattern, Callable],
+ attribute: Union[str, None] = None,
+ ) -> "CVTermList":
+ """Query the CVTermList and return a list of CVTerm objects.
+
+ Parameters
+ ----------
+ search_function : a string, regular expression or function
+ Used to find the matching elements in the list.
+ - a regular expression (possibly compiled), in which case the
+ given attribute of the object should match the regular expression.
+ - a function which takes one argument and returns True for
+ desired values
+
+ attribute : string or None
+ the name attribute of the object to passed as argument to the
+ `search_function`. If this is None and a regular expression/string is given,
+ will match the regular expression to both qualifier and resources.
+
+ Returns
+ -------
+ CVTermList
+ a new list of CVTerm objects which match the query
+
+ Examples
+ --------
+ >>> from cobra.io import load_model
+ >>> model = load_model('iJO1366')
+ >>> model.annotation.standardized.query('bqb', 'qualifier')
+ >>> import re
+ >>> regex = re.compile('^bqm')
+ >>> model.annotation.standardized.query(regex, 'qualifier')
+ """
+
+ def select_attribute(
+ x: CVTerm,
+ ) -> Union[CVTerm, ExternalResources, Qualifier, set]:
+ if attribute is None:
+ return x
+ else:
+ return getattr(x, attribute)
+
+ try:
+ # if the search_function is a regular expression
+ regex_searcher = re.compile(search_function)
+
+ if attribute is None:
+ attribute = ""
+
+ if attribute == "qualifier":
+ matches = [
+ cvterm
+ for cvterm in self.data
+ if regex_searcher.findall(select_attribute(cvterm).name) != []
+ ]
+ elif attribute == "resources":
+ matches = [
+ cvterm
+ for cvterm in self.data
+ if any(
+ regex_searcher.findall(res) for res in select_attribute(cvterm)
+ )
+ ]
+ elif attribute == "external_resources":
+ matches = [
+ cvterm
+ for cvterm in self.data
+ if any(
+ regex_searcher.findall(res)
+ for res in select_attribute(cvterm).resources
+ )
+ ]
+ else:
+ matches = [
+ cvterm
+ for cvterm in self.data
+ if regex_searcher.findall(cvterm.qualifier.name) != []
+ or any(regex_searcher.findall(res) for res in cvterm.resources)
+ ]
+ except TypeError:
+ matches = [
+ cvterm
+ for cvterm in self.data
+ if search_function(select_attribute(cvterm))
+ ]
+
+ results = self.__class__(matches)
+ return results
+
+ def __setitem__(self, key: int, value: Union[CVTerm, Dict]) -> None:
+ """Set item in CVTermList.
+
+ This function will check that it is a valid item, converting it to CVTerm if
+ necessary (see _check_CVTerm).
+
+ Parameters
+ ----------
+ key: int
+ value: CVTerm or dict
+ dict will be converted to CVTerm
+ """
+ UserList.__setitem__(self, key, self._check_CVTerm(value))
+
+ def append(self, item: Union[CVTerm, Dict]) -> None:
+ """Append CVTerm to end.
+
+ Parameters
+ ----------
+ item: CVTerm or dict
+ dict will be converted to CVTerm.
+ """
+ self._check_CVTerm(item)
+ UserList.append(self, item)
+
+ def extend(
+ self, iterable: Union["CVTermList", Iterable[Union[CVTerm, Dict]]]
+ ) -> None:
+ """Extend data list by appending elements from the iterable.
+
+ Parameters
+ ----------
+ iterable : Iterable
+ """
+ if isinstance(iterable, CVTermList):
+ self.data.extend(iterable.data)
+ elif isinstance(iterable, Iterable):
+ self.data.extend([self._check_CVTerm(i) for i in iterable])
+
+ def __eq__(self, other: [list, "CVTermList"]) -> bool:
+ """Compare two CVTermList objects to find out whether they are the same.
+
+ Equality is defined as them having the same data, but not necessarily the same
+ objects. If the given item is not a CVTermList or list, this function will
+ return False.
+
+ Parameters
+ ----------
+ other: CVTermList or list
+
+ Returns
+ -------
+ bool: True if the data matches, False otherwise
+ """
+ if isinstance(other, list):
+ return self.__eq__(CVTermList.from_data(other))
+ if not isinstance(other, CVTermList):
+ return False
+ if len(self.data) != len(other.data):
+ return False
+ for self_i, other_i in zip(self.data, other.data):
+ if self_i != other_i:
+ return False
+ return True
+
+ def _repr_html_(self) -> str:
+ """Generate CVTermList as HTML.
+
+ Returns
+ -------
+ str
+ HTML representation of the list of CVTerm resources.
+ """
+ return f"""CVTermList{"
".join([cvterm._repr_html_()
+ for cvterm in self.data])}"""
+
+
+class ExternalResources:
+ """Representation of a single set of resources and its nested annotation.
+
+ Each resource in the resources fields is a URI that uniquely identifies both the
+ resource and the data within the resource. Since a URI is not a URL, it does not
+ have to map to a physical Web object; it simply needs to identify, uniquely, a
+ controlled vocabulary term or database object.
+ These URIs are MIRIAM identifiers, following the format defined in
+ https://identifiers.org/.
+
+ The format allowed is
+ https://identifiers.org/[provider_code/]namespace:accession
+
+ The optional parameter provider_code denotes the Provider Code part of the Prefix.
+ It is trailed by a slash, to separate it from the required namespace,
+ which is followed by a colon and the accession.
+
+ Example Resources URIs
+ ----------------------
+ https://identifiers.org/pubmed:22140103
+ https://identifiers.org/ec-code:1.1.1.1
+
+ https://identifiers.org/epmc/pubmed:22140103
+ https://identifiers.org/expasy/ec-code:1.1.1.1
+
+
+ Parameters
+ ----------
+ resources: list or str
+ A list of URIs (resources)
+ nested_data : CVTermList
+ Nested annotation, in CVTermList format
+
+ Can also be created from dictionary, see ExternalResources.from_dict()
+ """
+
+ def __init__(
+ self,
+ resources: Optional[Union[List, str]] = None,
+ nested_data: Optional[Union[Dict, CVTerm, CVTermList]] = None,
+ ):
+ """Initialize ExternalResources object.
+
+ Parameters
+ ----------
+ resources: list or str, optional
+ A list of URIs (resources) or str. Str will be placed in a list if only
+ one resource is used.
+ nested_data : dict or CVTerm or CVTermList, optional
+ Nested annotation, in CVTermList format
+
+ See Also
+ --------
+ ExternalResources.resources()
+ ExternalResources.nested_data()
+ """
+ self._resources = None
+ self._nested_data = None
+ self.resources = resources
+ if resources:
+ self.nested_data = nested_data
+
+ @property
+ def resources(self) -> FrozenSet:
+ """Get resources of ExternalResources.
+
+ Returns
+ -------
+ frozenset:
+ The list of URIs in a frozenset.
+ """
+ return frozenset(self._resources)
+
+ @resources.setter
+ def resources(self, value: Union[List[str], str]) -> None:
+ """Set resources of ExternalResources.
+
+ Will set the URIs of ExternalResources.
+
+ Parameters
+ ----------
+ value: str or list
+ Should be list of URIs. If only one string is given, the function
+ assumes it is one URI, and it is placed in a list.
+ If None is given, the resources field is set to an empty list.
+
+ Raises
+ ------
+ TypeError
+ If value is neither list nor str.
+ """
+ if value is None:
+ value = []
+ if isinstance(value, list):
+ self._resources = value
+ elif isinstance(value, str):
+ self._resources = [value]
+ else:
+ raise TypeError(f"The resources must be a string or a list: {value}")
+
+ @property
+ def resource_nested(self) -> FrozenSet:
+ """Get resources, including resources of nested data.
+
+ This will get resources of the current ExternalResource and all resources
+ of nested data, if they exist.
+
+ Returns
+ -------
+ FrozenSet: a frozen set of URIs
+ """
+ resources = set()
+ resources.update(self.resources)
+ if self.nested_data:
+ resources.update(self.nested_data.resources)
+ return frozenset(resources)
+
+ @property
+ def nested_data(self) -> Optional[CVTermList]:
+ """Get nested data of ExternalResources.
+
+ Returns
+ -------
+ CVTermList: optional
+ Will return None if this ExternalResources object has no nested data.
+ """
+ return self._nested_data
+
+ @nested_data.setter
+ def nested_data(self, value: Optional[Union[Dict, List, CVTerm, CVTermList]]):
+ """Set nested data of ExternalResources.
+
+ This function will convert the given value to CVTermList as follows
+ - dict is converted to CVTerm via CVTerm.from_dict()
+ - list is converted via CVTermList.from_data()
+ - CVTerm is placed in a list and tranformed to CVTermList
+ - CVTermList is unchanged
+ - None will set the nested_data as an empty CVTermList (used for new
+ ExternalResources objects)
+
+ Parameters
+ ----------
+ value: dict or list or CVTerm or CVTermList, optional
+
+ Raises
+ ------
+ TypeError
+ If value is neither None, list, CVTerm or CVTermList.
+ """
+ if value is None:
+ self._nested_data = CVTermList()
+ elif isinstance(value, CVTerm):
+ self._nested_data = CVTermList([value])
+ elif isinstance(value, CVTermList):
+ self._nested_data = value
+ elif isinstance(value, list):
+ self._nested_data = CVTermList.from_data(value)
+ elif isinstance(value, dict):
+ self._nested_data = CVTermList.from_data(CVTerm.from_dict(value))
+ else:
+ raise TypeError(
+ f"The nested data structure does not have valid CVTerm format: {value}"
+ )
+
+ def to_dict(self):
+ """Generate a dict representing an ExternalResource object.
+
+ Returns
+ -------
+ dict
+ A dictionary with two keys
+ "resources" - sorted list of resources.
+ "nested_data" - optional, dict of nested_data. See CVTermList.to_dict()
+ """
+ ex_dic = {"resources": sorted(self._resources)}
+ if self.nested_data is not None and len(self.nested_data):
+ ex_dic["nested_data"] = self.nested_data.to_list_of_dicts()
+ return ex_dic
+
+ @classmethod
+ def from_dict(cls, input_data: Dict) -> "ExternalResources":
+ """Generate ExternalResources object from dict.
+
+ Parameters
+ ----------
+ input_data: dict
+ Accepts a dictionary as input that has two keys
+ "resources", optional a list of URIs
+ "nested_data", optional - nested data. Nested data must be a list,
+ CVTerm or CVTermList.
+
+ Returns
+ -------
+ ExternalResources
+
+ See Also
+ --------
+ ExternalResources.nested_data
+
+ """
+ ex_res = cls(
+ resources=input_data.get("resources", None),
+ nested_data=input_data.get("nested_data", None),
+ )
+ return ex_res
+
+ def __eq__(self, other: "ExternalResources") -> bool:
+ """Compare two ExternalResources object.
+
+ Compare two ExternalResources objects to find out whether
+ they are same (have same data) or not.
+
+ Returns
+ -------
+ bool
+ True if resources are equal in both objects, and both objects have the same
+ nested_data (None or identical CVTerm). False otherwise.
+ """
+ if self.resources != other.resources:
+ return False
+ if self.nested_data is None and other.nested_data is None:
+ return True
+ elif self.nested_data is None or other.nested_data is None:
+ return False
+ elif self.nested_data != other.nested_data:
+ return False
+ return True
+
+ def __str__(self) -> str:
+ """Return ExternalResources dictionary as str.
+
+ Returns
+ -------
+ str
+ String output of to_dict().
+
+ See Also
+ --------
+ ExternalResources.to_dict()
+ """
+ return str(self.to_dict())
+
+ def __repr__(self) -> str:
+ """Generate ExternalResources as str, with class.
+
+ Returns
+ -------
+ str
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__} "
+ f"{self.__str__()}"
+ )
+
+ def _repr_html_(self) -> str:
+ """Generate ExternalResources as HTML.
+
+ Returns
+ -------
+ str
+ HTML representation of the external resource.
+ """
+ html_rep = f"""
+
+ Resources{"
".join(self.resources)}
"""
+ if self.nested_data is not None and len(self.nested_data):
+ html_rep += f"""Nested Data{self.nested_data}
"""
+
+ html_rep += f"""
+ Memory address{id(self):#x}
+
"""
+ return html_rep
diff --git a/src/cobra/core/metadata/helper.py b/src/cobra/core/metadata/helper.py
new file mode 100644
index 000000000..9f1aa7e93
--- /dev/null
+++ b/src/cobra/core/metadata/helper.py
@@ -0,0 +1,45 @@
+"""Helper functions and properties for dealing with annotation data.
+
+This is a unification of helper functions from sbml.py and cvterm.py.
+
+"""
+import logging
+import re
+from typing import Tuple, Union
+
+
+LOGGER = logging.getLogger(__name__)
+
+__all__ = ["URL_IDENTIFIERS_PATTERN", "parse_identifiers_uri"]
+
+# the URL pattern to parse namespace and identifier
+URL_IDENTIFIERS_PATTERN = re.compile(r"^https?://identifiers.org/(.+?)[:/](.+)")
+
+
+def parse_identifiers_uri(uri: str) -> Union[None, Tuple[str, str]]:
+ """Parse namespace and term from given identifiers annotation uri.
+
+ Parameters
+ ----------
+ uri : str
+ uri (identifiers.org url)
+
+ Returns
+ -------
+ (namespace, identifier) if resolvable, None otherwise
+ """
+ match = URL_IDENTIFIERS_PATTERN.match(uri)
+ if match:
+ namespace, identifier = match.group(1), match.group(2)
+ if namespace.isupper():
+ identifier = f"{namespace}:{identifier}"
+ namespace = namespace.lower()
+ else:
+ LOGGER.warning(
+ f"{uri} does not conform to "
+ f"'http(s)://identifiers.org/collection/id' or"
+ f"'http(s)://identifiers.org/COLLECTION:id"
+ )
+ return None
+
+ return namespace, identifier
diff --git a/src/cobra/core/metadata/history.py b/src/cobra/core/metadata/history.py
new file mode 100644
index 000000000..8eb866eb7
--- /dev/null
+++ b/src/cobra/core/metadata/history.py
@@ -0,0 +1,392 @@
+"""Encodes History and Creator.
+
+The history allows to encode provenance meta-data about
+model objects. The history allows to encode who created or modified
+objects in a model with respective time stamps.
+"""
+import re
+from datetime import datetime
+from typing import Dict, Iterable, List, NamedTuple, Optional, Union
+
+
+STRTIME_FORMAT = "%Y-%m-%dT%H:%M:%S%z"
+
+
+class History:
+ """History object encoding object provenance.
+
+ Parameters
+ ----------
+ creators : list
+ A list of Creators
+ created_date : datetime
+ The datetime of creation in W3CDTF ISO 8601 format
+ modified_dates : list
+ A list of datetimes when the object was modified.
+ """
+
+ def __init__(
+ self,
+ creators: Optional[List["Creator"]] = None,
+ created_date: Optional[Union[datetime, str]] = None,
+ modified_dates: Optional[List[Union[datetime, str]]] = None,
+ ):
+ """Initialize the class.
+
+ Parameters
+ ----------
+ creators: list
+ list of Creator class. Optional, default None.
+ created_date: datetime
+ Created date. Optional, default None.
+ modified_dates: list
+ Dates when this annotation was modified. List of datetime dates or strings.
+ Optional, default None.
+ """
+ if modified_dates is None:
+ modified_dates = []
+ if creators is None:
+ creators = []
+ self._creators = []
+ self._created_date = None
+ self._modified_dates = []
+
+ # use properties to set fields
+ self.creators = creators
+ self.created_date = created_date
+ self.modified_dates = modified_dates
+
+ @property
+ def creators(self) -> List["Creator"]:
+ """Get creators for History.
+
+ Returns
+ -------
+ list
+ A list of Creator objects.
+ """
+ return self._creators
+
+ @creators.setter
+ def creators(self, values: Iterable[Union[Dict, "Creator"]]) -> None:
+ """Set creators for History.
+
+ Parameters
+ ----------
+ values: iterable
+ An iterable of dictionaries and/or Creator objects.
+ """
+ self._creators = [Creator.from_data(v) for v in values]
+
+ @staticmethod
+ def parse_datetime(value: Optional[Union[str, datetime]]) -> Optional[datetime]:
+ """Parse datetime into str.
+
+ Parameters
+ ----------
+ value: str or datetime
+ Optional. If None, the function will return None.
+ str is converted to datetime.
+ If given datetime, the format will be validated.
+
+ Returns
+ -------
+ datetime: optional
+ Returns None if given None.
+
+ Raises
+ ------
+ TypeError
+ If value is not None, or an instance of str, datetime.
+ """
+ if value is None:
+ return None
+ if isinstance(value, datetime):
+ return value
+ elif isinstance(value, str):
+ return History.date_from_str(value)
+ else:
+ raise TypeError(
+ f"Invalid type passed for datetime. "
+ f"Accepted types are 'str' or 'datetime' objects: {value}"
+ )
+
+ @staticmethod
+ def date_from_str(datetime_str: str) -> datetime:
+ """Validate if the date format is of type w3cdtf ISO 8601.
+
+ Parameters
+ ----------
+ datetime_str: str
+ Datetime in string format.
+
+ Returns
+ -------
+ datetime if valid format
+
+ Raises
+ ------
+ ValueError if not valid.
+ """
+ if not isinstance(datetime_str, str):
+ raise TypeError(f"The date passed must be of type string: {datetime_str}")
+
+ # python 3.6 doesn't allow : (colon) in the utc offset.
+ try:
+ datetime_return = datetime.strptime(datetime_str, STRTIME_FORMAT)
+ return datetime_return
+ except ValueError as e:
+ datetime_str = datetime_str.replace("Z", "+0000")
+ datetime_str = re.sub(r"(\+\d\d):(\d\d)\Z", "\\1\\2", datetime_str)
+ try:
+ datetime_return = datetime.strptime(datetime_str, STRTIME_FORMAT)
+ except ValueError:
+ raise ValueError(str(e))
+ return datetime_return
+
+ @property
+ def created_date(self) -> Optional[datetime]:
+ """Get created date for History.
+
+ Returns
+ -------
+ datetime
+ """
+ return self._created_date
+
+ @created_date.setter
+ def created_date(self, date: Union[str, "datetime"]) -> None:
+ """Set created date for History.
+
+ Parameters
+ ----------
+ date: str or datetime
+ """
+ self._created_date = self.parse_datetime(date)
+
+ @property
+ def modified_dates(self) -> List[datetime]:
+ """Get modified dates.
+
+ Returns
+ -------
+ list
+ List of datetimes when this annotation was modified, if any exist.
+ List can be empty.
+ """
+ return self._modified_dates
+
+ @modified_dates.setter
+ def modified_dates(self, dates: Iterable[Union[str, datetime]]) -> None:
+ """Set modified dates.
+
+ Parameters
+ -------
+ list
+ List of datetimes or strings when this annotation was modified.
+ """
+ self._modified_dates = [self.parse_datetime(d) for d in dates]
+
+ @staticmethod
+ def from_data(data: Union[Dict, "History"]) -> "History":
+ """Parse history from data.
+
+ Parameters
+ ----------
+ data: dict or History
+ Dict will be parsed to History object.
+
+ Returns
+ -------
+ History
+
+ Raises
+ ------
+ TypeError
+ If data is neither dict, History or None.
+ """
+ if data is None:
+ return History()
+ elif isinstance(data, History):
+ return data
+ elif isinstance(data, dict):
+ return History(**data)
+ else:
+ raise TypeError(f"Unsupported type for History: '{data}'")
+
+ def is_empty(self) -> bool:
+ """Check if history is empty.
+
+ Returns
+ -------
+ bool
+ Returns False if at least one history attribute is set, else True.
+ """
+ if self.creators:
+ return False
+ if self.created_date:
+ return False
+ if self.modified_dates:
+ return False
+ return True
+
+ def __eq__(self, other: "History") -> bool:
+ """Check equality of two history objects.
+
+ A history is equal if all attributes are equal.
+ If one and only one of self or other is empty will return False.
+ If both are empty, will return True.
+
+ Returns
+ -------
+ bool - True if equal, False otherwise.
+ """
+ if self.is_empty() and other.is_empty():
+ return True
+ elif (self.is_empty() and not other.is_empty()) or (
+ not self.is_empty() and other.is_empty()
+ ):
+ return False
+ # check equality of creators
+ if len(self.creators) != len(other.creators):
+ return False
+ for k, creator in enumerate(self.creators):
+ if creator != other.creators[k]:
+ return False
+
+ # checking equality of created_date
+ if self.created_date != other.created_date:
+ return False
+
+ # checking equality of modified_dates
+ if len(self.modified_dates) != len(other.modified_dates):
+ return False
+ for k, modified_date in enumerate(self.modified_dates):
+ if modified_date != other.modified_dates[k]:
+ return False
+
+ return True
+
+ def to_dict(self) -> Dict:
+ """Return dictionary representation of History.
+
+ Returns
+ -------
+ dict - Dictionary representation, of this format
+ {
+ "creators": list[dict]
+ "created_date": str
+ "modified_dates": list[str]
+ }
+ """
+ return {
+ "creators": [c.to_dict() for c in self.creators],
+ "created_date": self.created_date and self.created_date.isoformat(),
+ "modified_dates": [
+ mod_date.isoformat() for mod_date in self._modified_dates
+ ],
+ }
+
+ def __str__(self) -> str:
+ """Return a string representation.
+
+ Returns
+ -------
+ str
+ History in a flattened dictionary.
+ """
+ return str(self.to_dict())
+
+ def __repr__(self):
+ """Return a string with module and class name.
+
+ Returns
+ -------
+ str
+ History in a string, with module and class name.
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}"
+ f"({self.creators}, {self.created_date}, {self.modified_dates})"
+ )
+
+
+class Creator(NamedTuple):
+ """Metadata for person who created an object.
+
+ Parameters
+ ----------
+ given_name: str
+ Optional. Default None.
+ family_name: str
+ Optional. Default None.
+ email: str
+ Optional. Default None.
+ organisation: str
+ Optional. Default None.
+ """
+
+ given_name: Optional[str] = None
+ family_name: Optional[str] = None
+ email: Optional[str] = None
+ organisation: Optional[str] = None
+
+ @staticmethod
+ def from_data(data: Union[Dict, "Creator"]) -> "Creator":
+ """Parse creator from data.
+
+ Parameters
+ ----------
+ data: dict or Creator
+ Dictionary will be converted to Creator class.
+
+ Returns
+ -------
+ Creator - the creator in the Creator class
+ """
+ if not data:
+ return Creator()
+ elif isinstance(data, Creator):
+ return data
+ elif isinstance(data, dict):
+ return Creator(**data)
+ else:
+ raise TypeError(f"Invalid format for Creator: {data}")
+
+ def to_dict(self) -> Dict:
+ """Convert Creator to dictionary.
+
+ Returns
+ -------
+ dict in this format
+ {
+ "given_name": str,
+ "family_name": str,
+ "email": str,
+ "organisation": str,
+ }
+ """
+ return dict(self._asdict())
+
+ def __str__(self) -> str:
+ """Return string representation of Creator.
+
+ Returns
+ -------
+ str
+ String version of flattened dictionary.
+ """
+ return str(self.to_dict())
+
+ def __repr__(self):
+ """Return the Creator with module, class, and internal fields.
+
+ Returns
+ -------
+ str
+ """
+ return (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}"
+ f"('{self.given_name}', '{self.family_name}', '{self.email}', "
+ f"'{self.organisation}')"
+ )
diff --git a/src/cobra/core/metadata/metadata.py b/src/cobra/core/metadata/metadata.py
new file mode 100644
index 000000000..463139b6a
--- /dev/null
+++ b/src/cobra/core/metadata/metadata.py
@@ -0,0 +1,483 @@
+"""Define the cobra MetaData class."""
+
+from collections import OrderedDict
+from collections.abc import MutableMapping
+from datetime import datetime
+from typing import Dict, Iterable, Iterator, List, Optional, Union
+
+from ..metadata.custompairs import KeyValuePairs
+from ..metadata.cvterm import CVTerm, CVTermList
+from ..metadata.history import Creator, History
+
+
+class MetaData(MutableMapping):
+ """Meta-data of a cobrapy object.
+
+ Meta-data encodes additional information on an object such as annotations
+ or notes. Such information is currently stored in SBML on the notes and
+ annotation fields.
+
+ Meta-data consists of four components:
+ - standardized: storing resource:identifier annotation information in a CVTermList
+ object. The annotation information is exposed via the dict interface for
+ full backwards compatibility to the earlier object.annotation field. See
+ CVTermList.annotations() and MetaData.annotations()
+ - sbo - a single SBO term for the object. Can theoretically be placed in
+ standardized, but the most descriptive term should be kept in sbo. Right now,
+ cobrapy doesn't allow multiple sbo terms.
+ - History: storing the object history consisting of creators, created date, and
+ modified dates.
+ - custompairs (KeyValuePairs), a list of key-value pairs to
+ store additional information
+
+ Parameters
+ ----------
+ cvterms : dict or CVTermList object
+ The standardized store annotations to external resources
+ history : dict, History
+ The history stores information about the creator,
+ created and modified dates.
+ sbo: str
+ The sbo term to use for the entity. If you want to use more than one SBO term
+ (not recommended), use SBO in identifers.org format and put it in standardized.
+ keyvaluepairs : list
+ Key-value pairs which are not suitable to be
+ represented anywhere else in the model.
+ Data is represented as an OrderedDict.
+ """
+
+ def __init__(
+ self,
+ cvterms: Union[Dict, CVTermList] = None,
+ history: Union[Dict, History] = None,
+ sbo: str = "",
+ keyvaluepairs: List = None,
+ ):
+ """Initialize the MetaData class.
+
+ Parameters
+ ---------
+ cvterms : dict or CVTermList, optional
+ Which controlled vocabulary terms does the metadata have. Default None.
+ history: dict or History, optional
+ History of annotation, including creation data, creators, and optional
+ modificiation date. Default None.
+ sbo: str
+ SBO term, if relevant. Default "".
+ keyvaluepairs: KeyValuePairs
+ For annotations that don't match the identifiers.org format.
+
+ """
+ self._standardized = CVTermList.from_data(cvterms)
+ self._history = History.from_data(history)
+ self._custompairs = KeyValuePairs(keyvaluepairs)
+ self._sbo = sbo
+
+ # use setters
+ self.sbo = sbo
+ self.standardized = cvterms
+ self.history = history
+ self.custompairs = keyvaluepairs
+
+ @property
+ def standardized(self) -> "CVTermList":
+ """Get standardized field of MetaData.
+
+ Returns
+ -------
+ CVTermList
+ """
+ return self._standardized
+
+ @standardized.setter
+ def standardized(self, cvterms: Union[Dict, CVTermList]) -> None:
+ """Set standardized field of MetaData with controlled vocabulary (CVTerm).
+
+ Parameters
+ ----------
+ cvterms: dict or CVTermList
+ dict is converted to CVTermList using CVTermList.from_data().
+ The wrong type will lead to a TypeError being raised.
+ """
+ self._standardized = CVTermList.from_data(cvterms)
+
+ def add_cvterms(self, cvterms: Iterable[Union[Dict, CVTerm]]) -> None:
+ """Add one or more CVTerm objects to the standardized field.
+
+ This method will add CVTerm objects to the standardized field.
+
+ Parameters
+ ----------
+ cvterms: Iterable
+ An iterable of CVTerm objects or CVTerm dict compatible objects.
+ CVTermList is an acceptable Iterable in this case.
+
+ See Also
+ --------
+ CVTermList.add_cvterms()
+ """
+ self._standardized.add_cvterms(cvterms)
+
+ @property
+ def annotations(self) -> Dict:
+ """Backwards compatible annotations."""
+ anno_dict = self.standardized.annotations
+ if self.sbo:
+ anno_dict["sbo"] = self.sbo
+ return anno_dict
+
+ @property
+ def history(self) -> History:
+ """Get history of the object.
+
+ Returns
+ -------
+ History
+ """
+ return self._history
+
+ @history.setter
+ def history(self, history: Optional[Union[Dict, History]]) -> None:
+ """Set history of the object.
+
+ Parameters
+ ----------
+ history: History or dict or None
+ If None is given, will set the History to be empty.
+ Dict is converted via History.from_data()
+ """
+ self._history = History.from_data(history)
+
+ def add_creators(self, creators: Iterable[Union[Creator, dict]]) -> None:
+ """Add one or more creators to the object history.
+
+ The creators will be parsed and need to be a Creator object or a dictionary
+ in the correct format.
+
+ Parameters
+ ----------
+ creators: Iterable of dict or Creator
+ An iterable of dicts or Creator objects.
+
+ See Also
+ --------
+ Creator.from_data()
+ """
+ self.history.creators.extend(
+ [Creator.from_data(creator) for creator in creators]
+ )
+
+ def add_modification_dates(
+ self, dates: Union[datetime, str, Iterable[Union[datetime, str]]]
+ ) -> None:
+ """Add modification dates to the object history.
+
+ The dates will be parsed and need to be string in the acceptable format or
+ datetime.
+
+ Parameters
+ ----------
+ dates: Iterable or str or datetime
+ An iterable of strings or datetime objects, or one str or one datetime.
+
+ See Also
+ --------
+ History.parse_datetime()
+ """
+ if isinstance(dates, (str, datetime)):
+ dates = [dates]
+ self.history.modified_dates.extend([History.parse_datetime(d) for d in dates])
+
+ @property
+ def sbo(self) -> str:
+ """Return the SBO term of the MetaData.
+
+ Returns
+ -------
+ str: SBO as string
+ """
+ return self._sbo
+
+ @sbo.setter
+ def sbo(self, value: str) -> None:
+ """Set the SBO term."""
+ if isinstance(value, list):
+ value = value[0]
+ self._sbo = value
+
+ @property
+ def keyvaluepairs(self) -> KeyValuePairs:
+ return self._custompairs
+
+ @keyvaluepairs.setter
+ def keyvaluepairs(self, keyvaluepairs: Union[Dict, KeyValuePairs]) -> None:
+ self._custompairs = KeyValuePairs(keyvaluepairs)
+
+ def __setitem__(self, key: str, value: Union[List, str]) -> None:
+ """Set the item for accessing metadata as dict (the old style annotation).
+
+ Parameters
+ ----------
+ key: str
+ provider key word.
+ value: List or str
+ A str that is one term or a list that will contain multiple terms
+
+ This function will first delete the existing value for the key, and then set
+ it to the new value. Be careful - if you give this function incorrect input,
+ the deletion will happen anyway, and the value of the key will be empty!
+
+ If the key is sbo, sets the self.sbo term to the first item in the list. The
+ rest of the items in the list are ignored.
+ Cobrapy support for multiple SBO terms is not implemented yet.
+
+ See Also
+ --------
+ `CVTermList().add_simple_annotations()`
+ """
+ if key == "sbo":
+ if isinstance(value, list):
+ value = value[0]
+ self.sbo = value
+ else:
+ self.__delitem__(key)
+ self._standardized.add_simple_annotations(dict({key: value}))
+
+ def __getitem__(self, key: str) -> List:
+ """Get item using old annotation type dictionary.
+
+ If the key is sbo, will return the sbo field directly.
+ Otherwise, will query the annotations (old style) dictionary.
+
+ Note, that __setitem__, __getitem__ and __delitem__ will ignore custompairs. If
+ you want to edit that field, use relevant functions for it.
+
+ Parameters
+ ----------
+ key: str
+ provider key word.
+
+ Returns
+ -------
+ list
+ """
+ if key == "sbo":
+ return [self.sbo]
+ else:
+ return self.annotations[key]
+
+ def __delitem__(self, key: str) -> None:
+ """Delete item using old annotation type dictionary as reference.
+
+ If the key is sbo, will zero out the sbo field directly to an empty string.
+ Otherwise, will delete from the annotations (old style) dictionary, using
+ the value as a pattern to search in CVTermList resources.
+ See `CVTermList.delete_simple_annotation()`
+
+ Parameters
+ ----------
+ key: str
+ provider key word.
+
+ Note, that __setitem__, __getitem__ and __delitem__ will ignore custompairs. If
+ you want to edit that field, use relevant functions for it.
+ """
+ if key == "sbo":
+ self.sbo = ""
+ else:
+ self._standardized.delete_annotation(key)
+
+ def __eq__(self, other: Union["MetaData", Dict]) -> bool:
+ """Compare two MetaData objects to find out whether they are the same.
+
+ If given a dict, the dictionary is converted to MetaData and then compared.
+
+ Equality is defined in two ways, depending if history and custompairs exist.
+ 1) If history or custompairs exist and are not empty/None, the two objects are
+ equal (the function will return True) if
+ - standardized (CVTermList) are equal
+ - all attributes of the history (History) are equal
+ - custompairs are identical
+ If one of these three conditions is not true, the function will return False.
+ 2) If only standardized exist, while history and custompairs are empty
+ (history.is_empty() is True and custompairs is None) for both objects,
+ then the annotations field (CVTermList.annotations()) is compared as two
+ dictionaries.
+
+ Parameters
+ ----------
+ other: MetaData or dict
+
+ Returns
+ -------
+ bool: True if equal, False otherwise.
+ """
+ if isinstance(other, dict):
+ return self == MetaData.from_dict(other)
+ if (
+ self.standardized
+ and self.history.is_empty()
+ and not self.custompairs
+ and other.standardized
+ and other.history.is_empty()
+ and not other.custompairs
+ ):
+ return self.annotations == other.annotations
+
+ return (
+ (self.standardized == other.standardized)
+ and (self.history == other.history)
+ and (self.custompairs == other.custompairs)
+ )
+
+ def __ne__(self, other) -> bool:
+ """Define not-equal to override default.
+
+ Parameters
+ ----------
+ other: MetaData or dict
+
+ Returns
+ -------
+ bool: False if equal, True otherwise.
+
+ See Also
+ --------
+ MetaData.__eq__()
+ """
+ return not self.__eq__(other)
+
+ def __iter__(self) -> Iterator:
+ """Iterate over the MetaData annotations dict.
+
+ This function will iterate over the annotations (old-style) dictionary.
+
+ Returns
+ -------
+ Iterator
+ """
+ return iter(self.annotations)
+
+ def __len__(self) -> int:
+ """Return the length of the MetaData annotations dict.
+
+ The length of the annotations dict will be returned as a int.
+
+ Returns
+ -------
+ int
+ result of running len on the annotations dict
+ """
+ return len(self.annotations)
+
+ def __str__(self) -> str:
+ """Return the MetaData as str.
+
+ The annotations dict will be returned as a string. This does not include all
+ of the possible MetaData fields.
+
+ Returns
+ -------
+ str
+ """
+ return str(dict(self.annotations))
+
+ def __repr__(self) -> str:
+ """Return the MetaData as str with module, class, and code to recreate it.
+
+ If MetaData has standardized, history or custompairs, the dictionary will
+ contain them as keys.
+ If not, the dictionary will have only the annotations dictionary.
+ In either case, if sbo field is set, it will be outputted in the dictionary.
+
+ Returns
+ -------
+ str
+
+ See Also
+ --------
+ MetaData.from_dict()
+ """
+ repr_str = (
+ f"{self.__class__.__module__}.{self.__class__.__qualname__}.from_dict("
+ )
+ cvterms = self.standardized
+ history = self.history
+ keyValuepairs = self.keyvaluepairs
+
+ if cvterms or not history.is_empty() or keyValuepairs:
+ repr_str += (
+ f"'standardized': {self.standardized.to_list_of_dicts()},"
+ f"'history': {self.history.to_dict()},"
+ f"'custompairs': {self.custompairs},"
+ )
+ if self.sbo:
+ repr_str += f"'sbo': {self.sbo})"
+ else:
+ anno_dict = self.annotations
+ if self.sbo:
+ anno_dict.update({"sbo": self.sbo})
+ repr_str += f"{anno_dict})"
+ return repr_str
+
+ def to_dict(self) -> Dict:
+ """Create string dictionary for serialization.
+
+ Returns
+ -------
+ dict
+ """
+ d = OrderedDict()
+ if self.sbo:
+ # set first SBO term as sbo
+ d["sbo"] = self.sbo
+
+ if self.standardized:
+ d["standardized"] = self.standardized.to_list_of_dicts()
+
+ if self.history and not self.history.is_empty():
+ d["history"] = self.history.to_dict()
+
+ if self.keyvaluepairs:
+ d["custompairs"] = self.keyvaluepairs.to_dict()
+
+ return d
+
+ @staticmethod
+ def from_dict(data: Dict) -> "MetaData":
+ """Generate MetaData from dictionary.
+
+ This function has two options
+ 1) If the dictionary has standardized, history, or custompairs, it uses
+ the relevant fields to create MetaData.
+ 2) If the dictionary has none of the above fields, it creates an empty
+ MetaData object, and then fills it using CVTermList.add_simple_annotation()
+ where the keys are namespaces and the values are identifiers.
+ In this case, all qualifiers will be "bqb_is".
+
+ In either case, if "sbo" is present as one of the keys, this will fill the sbo
+ field of the MetaData using the value of "sbo" key.
+
+ Parameters
+ ----------
+ data: dict
+ Dictionary to transform into MetaData.
+
+ Returns
+ -------
+ MetaData
+ """
+ cvterms = data.get("standardized", None)
+ history = data.get("history", None)
+ keyValuepairs = data.get("custompairs", None)
+
+ if cvterms or history or keyValuepairs:
+ annotation = MetaData(cvterms, history, keyValuepairs)
+ else:
+ annotation = MetaData()
+ annotation.standardized.add_simple_annotations(data)
+
+ if "sbo" in data:
+ annotation["sbo"] = data["sbo"]
+
+ return annotation
diff --git a/src/cobra/core/model.py b/src/cobra/core/model.py
index 5abf5acaf..e332c44c5 100644
--- a/src/cobra/core/model.py
+++ b/src/cobra/core/model.py
@@ -324,7 +324,7 @@ def copy(self):
"reactions",
"genes",
"notes",
- "annotation",
+ "_annotation",
"groups",
}
for attr in self.__dict__:
@@ -334,13 +334,14 @@ def copy(self):
new.annotation = deepcopy(self.annotation)
new.metabolites = DictList()
- do_not_copy_by_ref = {"_reaction", "_model"}
+ do_not_copy_by_ref = {"_reaction", "_model", "_annotation"}
for metabolite in self.metabolites:
new_met = metabolite.__class__()
for attr, value in metabolite.__dict__.items():
if attr not in do_not_copy_by_ref:
new_met.__dict__[attr] = copy(value) if attr == "formula" else value
new_met._model = new
+ new_met.annotation = deepcopy(metabolite.annotation)
new.metabolites.append(new_met)
new.genes = DictList()
@@ -352,16 +353,18 @@ def copy(self):
copy(value) if attr == "formula" else value
)
new_gene._model = new
+ new_gene.annotation = deepcopy(gene.annotation)
new.genes.append(new_gene)
new.reactions = DictList()
- do_not_copy_by_ref = {"_model", "_metabolites", "_genes"}
+ do_not_copy_by_ref = {"_model", "_metabolites", "_genes", "_annotation"}
for reaction in self.reactions:
new_reaction = reaction.__class__()
for attr, value in reaction.__dict__.items():
if attr not in do_not_copy_by_ref:
new_reaction.__dict__[attr] = copy(value)
new_reaction._model = new
+ new_reaction._annotation = deepcopy(reaction.annotation)
new.reactions.append(new_reaction)
# update awareness
for metabolite, stoic in reaction._metabolites.items():
@@ -371,7 +374,7 @@ def copy(self):
new_reaction.update_genes_from_gpr()
new.groups = DictList()
- do_not_copy_by_ref = {"_model", "_members"}
+ do_not_copy_by_ref = {"_model", "_members", "_annotation"}
# Groups can be members of other groups. We initialize them first and
# then update their members.
for group in self.groups:
@@ -380,6 +383,7 @@ def copy(self):
if attr not in do_not_copy_by_ref:
new_group.__dict__[attr] = copy(value)
new_group._model = new
+ new_group.annotation = deepcopy(group.annotation)
new.groups.append(new_group)
for group in self.groups:
new_group = new.groups.get_by_id(group.id)
@@ -393,7 +397,7 @@ def copy(self):
elif isinstance(member, Gene):
new_object = new.genes.get_by_id(member.id)
elif isinstance(member, Group):
- new_object = new.genes.get_by_id(member.id)
+ new_object = new.groups.get_by_id(member.id)
else:
raise TypeError(
"The group member {!r} is unexpectedly not a "
diff --git a/src/cobra/core/object.py b/src/cobra/core/object.py
index 78d092d05..fb75c2777 100644
--- a/src/cobra/core/object.py
+++ b/src/cobra/core/object.py
@@ -2,6 +2,8 @@
from typing import Optional
+from cobra.core.metadata import MetaData
+
class Object:
"""Defines common behavior of object in cobra.core."""
@@ -23,7 +25,7 @@ def __init__(self, id: Optional[str] = None, name: str = "") -> None:
self.name = name
self.notes = {}
- self._annotation = {}
+ self._annotation = MetaData()
@property
def id(self) -> str:
@@ -70,7 +72,7 @@ def _set_id_with_model(self, value) -> None:
self._id = value
@property
- def annotation(self) -> dict:
+ def annotation(self) -> MetaData:
"""Get annotation dictionary.
Returns
@@ -93,10 +95,15 @@ def annotation(self, annotation):
------
TypeError if annotation not a dict.
"""
- if not isinstance(annotation, dict):
- raise TypeError("Annotation must be a dict")
- else:
+ if isinstance(annotation, MetaData):
self._annotation = annotation
+ elif isinstance(annotation, dict):
+ self._annotation = MetaData().from_dict(annotation)
+ else:
+ raise TypeError(
+ f"The data passed for annotation must be inside "
+ f"a dictionary or MetaData: {annotation}"
+ )
def __getstate__(self) -> dict:
"""Get state of annotation.
diff --git a/src/cobra/data/mini.json b/src/cobra/data/mini.json
index df70c0a4f..35421b87d 100644
--- a/src/cobra/data/mini.json
+++ b/src/cobra/data/mini.json
@@ -5,1120 +5,1195 @@
},
"genes": [
{
- "id": "b0755",
+ "id": "G_b0755",
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{
- "id": "b0875",
+ "id": "G_b0875",
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},
{
- "id": "b1101",
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},
{
- "id": "b1380",
+ "id": "G_b1380",
"name": "ldhA"
},
{
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+ "id": "G_b1621",
"name": "malX"
},
{
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- "ncbiprotein": [
- "1208453",
- "1652654"
- ]
+ "standardized": {
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+ {
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+ "http://identifiers.org/ncbiprotein/1652654"
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+ }
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},
{
- "id": "b1723",
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{
- "id": "b1773",
+ "id": "G_b1773",
"name": "ydjI"
},
{
- "id": "b1779",
+ "id": "G_b1779",
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},
{
- "id": "b1817",
+ "id": "G_b1817",
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},
{
- "id": "b1818",
+ "id": "G_b1818",
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},
{
- "id": "b1819",
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},
{
- "id": "b1854",
+ "id": "G_b1854",
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},
{
- "id": "b2097",
+ "id": "G_b2097",
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},
{
- "id": "b2133",
+ "id": "G_b2133",
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},
{
- "id": "b2415",
+ "id": "G_b2415",
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},
{
- "id": "b2416",
+ "id": "G_b2416",
"name": "ptsI"
},
{
- "id": "b2417",
+ "id": "G_b2417",
"name": "crr"
},
{
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- "ncbiprotein": "1653839"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
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+ ]
+ }
+ ]
+ }
},
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+ "id": "G_b2779",
"name": "eno"
},
{
- "id": "b2925",
+ "id": "G_b2925",
"name": "fbaA"
},
{
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- "ncbiprotein": "1653609"
+ "standardized": {
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+ {
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+ }
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+ }
},
- "id": "b2926",
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{
- "id": "b2987",
+ "id": "G_b2987",
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},
{
- "id": "b3493",
+ "id": "G_b3493",
"name": "pitA"
},
{
- "id": "b3612",
+ "id": "G_b3612",
"name": "gpmM"
},
{
"annotation": {
- "ncbiprotein": [
- "1006614",
- "1651919"
- ]
+ "standardized": {
+ "bqb_is": [
+ {
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+ "http://identifiers.org/ncbiprotein/1651919"
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+ }
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},
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"name": "pfkA"
},
{
- "id": "b3919",
+ "id": "G_b3919",
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},
{
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+ "standardized": {
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+ {
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},
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{
- "id": "b4395",
+ "id": "G_b4395",
"name": "ytjC"
},
{
- "id": "s0001",
+ "id": "G_s0001",
"name": "G_s0001"
}
],
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{
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- "CHEBI:1658",
- "CHEBI:20189",
- "CHEBI:57604",
- "CHEBI:11881"
- ],
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- "pubchem.substance": "3535",
- "reactome": "REACT_29800",
- "seed.compound": "cpd00203",
- "unipathway.compound": "UPC00236"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
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+ "http://identifiers.org/biocyc/DPG",
+ "http://identifiers.org/chebi/CHEBI:16001",
+ "http://identifiers.org/chebi/CHEBI:1658",
+ "http://identifiers.org/chebi/CHEBI:20189",
+ "http://identifiers.org/chebi/CHEBI:57604",
+ "http://identifiers.org/chebi/CHEBI:11881",
+ "http://identifiers.org/hmdb/HMDB01270",
+ "http://identifiers.org/kegg.compound/C00236",
+ "http://identifiers.org/pubchem.substance/3535",
+ "http://identifiers.org/reactome/REACT_29800",
+ "http://identifiers.org/seed.compound/cpd00203",
+ "http://identifiers.org/unipathway.compound/UPC00236"
+ ]
+ }
+ ]
+ }
},
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"compartment": "c",
"formula": "C3H4O10P2",
- "id": "13dpg_c",
+ "id": "M_13dpg_c",
"name": "3-Phospho-D-glyceroyl phosphate"
},
{
"annotation": {
- "bigg.metabolite": "2pg",
- "biocyc": "2-PG",
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- "CHEBI:58289",
- "CHEBI:17835",
- "CHEBI:21028",
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- "CHEBI:12986",
- "CHEBI:24344",
- "CHEBI:39868"
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- "reactome": "REACT_30485",
- "seed.compound": "cpd00482",
- "unipathway.compound": "UPC00631"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.metabolite/2pg",
+ "http://identifiers.org/biocyc/2-PG",
+ "http://identifiers.org/chebi/CHEBI:1267",
+ "http://identifiers.org/chebi/CHEBI:58289",
+ "http://identifiers.org/chebi/CHEBI:17835",
+ "http://identifiers.org/chebi/CHEBI:21028",
+ "http://identifiers.org/chebi/CHEBI:11651",
+ "http://identifiers.org/chebi/CHEBI:12986",
+ "http://identifiers.org/chebi/CHEBI:24344",
+ "http://identifiers.org/chebi/CHEBI:39868",
+ "http://identifiers.org/hmdb/HMDB03391",
+ "http://identifiers.org/hmdb/HMDB00362",
+ "http://identifiers.org/kegg.compound/C00631",
+ "http://identifiers.org/pubchem.substance/3904",
+ "http://identifiers.org/reactome/REACT_30485",
+ "http://identifiers.org/seed.compound/cpd00482",
+ "http://identifiers.org/unipathway.compound/UPC00631"
+ ]
+ }
+ ]
+ }
},
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"formula": "C3H4O7P",
- "id": "2pg_c",
+ "id": "M_2pg_c",
"name": "D-Glycerate 2-phosphate"
},
{
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- "CHEBI:11879",
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- "CHEBI:17050",
- "CHEBI:21029",
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- "CHEBI:11880",
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- "CHEBI:17794",
- "CHEBI:24345"
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- "seed.compound": "cpd00169",
- "unipathway.compound": [
- "UPC00597",
- "UPC00197"
- ]
+ "standardized": {
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+ {
+ "resources": [
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+ "http://identifiers.org/biocyc/G3P",
+ "http://identifiers.org/chebi/CHEBI:40016",
+ "http://identifiers.org/chebi/CHEBI:58272",
+ "http://identifiers.org/chebi/CHEBI:57998",
+ "http://identifiers.org/chebi/CHEBI:11879",
+ "http://identifiers.org/chebi/CHEBI:1657",
+ "http://identifiers.org/chebi/CHEBI:1659",
+ "http://identifiers.org/chebi/CHEBI:17050",
+ "http://identifiers.org/chebi/CHEBI:21029",
+ "http://identifiers.org/chebi/CHEBI:11882",
+ "http://identifiers.org/chebi/CHEBI:11880",
+ "http://identifiers.org/chebi/CHEBI:12987",
+ "http://identifiers.org/chebi/CHEBI:17794",
+ "http://identifiers.org/chebi/CHEBI:24345",
+ "http://identifiers.org/hmdb/HMDB00807",
+ "http://identifiers.org/kegg.compound/C00197",
+ "http://identifiers.org/kegg.compound/C00597",
+ "http://identifiers.org/pubchem.substance/3497",
+ "http://identifiers.org/reactome/REACT_29728",
+ "http://identifiers.org/seed.compound/cpd00169",
+ "http://identifiers.org/unipathway.compound/UPC00597",
+ "http://identifiers.org/unipathway.compound/UPC00197"
+ ]
+ }
+ ]
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},
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"compartment": "c",
"formula": "C3H4O7P",
- "id": "3pg_c",
+ "id": "M_3pg_c",
"name": "3-Phospho-D-glycerate"
},
{
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- "CHEBI:16761",
- "CHEBI:2342",
- "CHEBI:22244",
- "CHEBI:40553",
- "CHEBI:456216"
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- "REACT_114564",
- "REACT_114565",
- "REACT_429153"
- ],
- "seed.compound": "cpd00008",
- "unipathway.compound": "UPC00008"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
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+ "http://identifiers.org/biocyc/ADP",
+ "http://identifiers.org/biocyc/ADP-GROUP",
+ "http://identifiers.org/cas/58-64-0",
+ "http://identifiers.org/cas/58-64-0",
+ "http://identifiers.org/chebi/CHEBI:13222",
+ "http://identifiers.org/chebi/CHEBI:16761",
+ "http://identifiers.org/chebi/CHEBI:2342",
+ "http://identifiers.org/chebi/CHEBI:22244",
+ "http://identifiers.org/chebi/CHEBI:40553",
+ "http://identifiers.org/chebi/CHEBI:456216",
+ "http://identifiers.org/hmdb/HMDB01341",
+ "http://identifiers.org/kegg.compound/C00008",
+ "http://identifiers.org/kegg.glycan/G11113",
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+ "http://identifiers.org/reactome/REACT_190072",
+ "http://identifiers.org/reactome/REACT_481002",
+ "http://identifiers.org/reactome/REACT_211606",
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+ "http://identifiers.org/reactome/REACT_29370",
+ "http://identifiers.org/reactome/REACT_196180",
+ "http://identifiers.org/reactome/REACT_113581",
+ "http://identifiers.org/reactome/REACT_113582",
+ "http://identifiers.org/reactome/REACT_114564",
+ "http://identifiers.org/reactome/REACT_114565",
+ "http://identifiers.org/reactome/REACT_429153",
+ "http://identifiers.org/seed.compound/cpd00008",
+ "http://identifiers.org/unipathway.compound/UPC00008"
+ ]
+ }
+ ]
+ }
},
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"compartment": "c",
"formula": "C10H12N5O10P2",
- "id": "adp_c",
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"name": "ADP"
},
{
"annotation": {
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- "biocyc": "ATP",
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- "CHEBI:15422",
- "CHEBI:57299",
- "CHEBI:13236",
- "CHEBI:10789",
- "CHEBI:30616",
- "CHEBI:22249",
- "CHEBI:10841",
- "CHEBI:2359"
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- "REACT_139836",
- "REACT_211579"
- ],
- "seed.compound": "cpd00002",
- "unipathway.compound": "UPC00002"
+ "standardized": {
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+ {
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+ "http://identifiers.org/biocyc/ATP",
+ "http://identifiers.org/cas/56-65-5",
+ "http://identifiers.org/cas/56-65-5",
+ "http://identifiers.org/chebi/CHEBI:40938",
+ "http://identifiers.org/chebi/CHEBI:15422",
+ "http://identifiers.org/chebi/CHEBI:57299",
+ "http://identifiers.org/chebi/CHEBI:13236",
+ "http://identifiers.org/chebi/CHEBI:10789",
+ "http://identifiers.org/chebi/CHEBI:30616",
+ "http://identifiers.org/chebi/CHEBI:22249",
+ "http://identifiers.org/chebi/CHEBI:10841",
+ "http://identifiers.org/chebi/CHEBI:2359",
+ "http://identifiers.org/hmdb/HMDB00538",
+ "http://identifiers.org/kegg.compound/C00002",
+ "http://identifiers.org/kegg.drug/D08646",
+ "http://identifiers.org/pubchem.substance/3304",
+ "http://identifiers.org/reactome/REACT_190078",
+ "http://identifiers.org/reactome/REACT_113592",
+ "http://identifiers.org/reactome/REACT_113593",
+ "http://identifiers.org/reactome/REACT_114570",
+ "http://identifiers.org/reactome/REACT_29358",
+ "http://identifiers.org/reactome/REACT_389573",
+ "http://identifiers.org/reactome/REACT_139836",
+ "http://identifiers.org/reactome/REACT_211579",
+ "http://identifiers.org/seed.compound/cpd00002",
+ "http://identifiers.org/unipathway.compound/UPC00002"
+ ]
+ }
+ ]
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},
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"compartment": "c",
"formula": "C10H12N5O13P3",
- "id": "atp_c",
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"name": "ATP"
},
{
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- "biocyc": "DIHYDROXY-ACETONE-PHOSPHATE",
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- "CHEBI:39571"
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- "REACT_75970",
- "REACT_390404"
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- "unipathway.compound": "UPC00111"
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+ "resources": [
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+ "http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE",
+ "http://identifiers.org/cas/57-04-5",
+ "http://identifiers.org/cas/57-04-5",
+ "http://identifiers.org/chebi/CHEBI:14341",
+ "http://identifiers.org/chebi/CHEBI:57642",
+ "http://identifiers.org/chebi/CHEBI:14342",
+ "http://identifiers.org/chebi/CHEBI:16108",
+ "http://identifiers.org/chebi/CHEBI:5454",
+ "http://identifiers.org/chebi/CHEBI:24355",
+ "http://identifiers.org/chebi/CHEBI:39571",
+ "http://identifiers.org/hmdb/HMDB01473",
+ "http://identifiers.org/hmdb/HMDB11735",
+ "http://identifiers.org/kegg.compound/C00111",
+ "http://identifiers.org/pubchem.substance/3411",
+ "http://identifiers.org/reactome/REACT_188451",
+ "http://identifiers.org/reactome/REACT_75970",
+ "http://identifiers.org/reactome/REACT_390404",
+ "http://identifiers.org/seed.compound/cpd00095",
+ "http://identifiers.org/unipathway.compound/UPC00111"
+ ]
+ }
+ ]
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},
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"compartment": "c",
"formula": "C3H5O6P",
- "id": "dhap_c",
+ "id": "M_dhap_c",
"name": "Dihydroxyacetone phosphate"
},
{
"annotation": {
- "bigg.metabolite": "f6p",
- "biocyc": "FRUCTOSE-6P",
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- "CHEBI:12352",
- "CHEBI:45804",
- "CHEBI:61527",
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- "CHEBI:10375",
- "CHEBI:16084",
- "CHEBI:42378",
- "CHEBI:22768"
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- "seed.compound": "cpd00072",
- "unipathway.compound": [
- "UPC05345",
- "UPC00085"
- ]
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
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+ "http://identifiers.org/biocyc/FRUCTOSE-6P",
+ "http://identifiers.org/cas/643-13-0",
+ "http://identifiers.org/cas/643-13-0",
+ "http://identifiers.org/chebi/CHEBI:57634",
+ "http://identifiers.org/chebi/CHEBI:12352",
+ "http://identifiers.org/chebi/CHEBI:45804",
+ "http://identifiers.org/chebi/CHEBI:61527",
+ "http://identifiers.org/chebi/CHEBI:61553",
+ "http://identifiers.org/chebi/CHEBI:10375",
+ "http://identifiers.org/chebi/CHEBI:16084",
+ "http://identifiers.org/chebi/CHEBI:42378",
+ "http://identifiers.org/chebi/CHEBI:22768",
+ "http://identifiers.org/hmdb/HMDB03971",
+ "http://identifiers.org/kegg.compound/C05345",
+ "http://identifiers.org/kegg.compound/C00085",
+ "http://identifiers.org/pubchem.substance/3385",
+ "http://identifiers.org/seed.compound/cpd00072",
+ "http://identifiers.org/unipathway.compound/UPC05345",
+ "http://identifiers.org/unipathway.compound/UPC00085"
+ ]
+ }
+ ]
+ }
},
"charge": -2,
"compartment": "c",
"formula": "C6H11O9P",
- "id": "f6p_c",
+ "id": "M_f6p_c",
"name": "D-Fructose 6-phosphate"
},
{
"annotation": {
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- "biocyc": "FRUCTOSE-16-DIPHOSPHATE",
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- "CHEBI:49299",
- "CHEBI:42553",
- "CHEBI:32966",
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- "CHEBI:28013",
- "CHEBI:32967",
- "CHEBI:41014",
- "CHEBI:22767",
- "CHEBI:10374",
- "CHEBI:40595",
- "CHEBI:40591"
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- "kegg.compound": [
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- "C00354"
- ],
- "pubchem.substance": "3647",
- "seed.compound": "cpd00290",
- "unipathway.compound": "UPC00354"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
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+ "http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE",
+ "http://identifiers.org/cas/488-69-7",
+ "http://identifiers.org/cas/488-69-7",
+ "http://identifiers.org/chebi/CHEBI:32968",
+ "http://identifiers.org/chebi/CHEBI:49299",
+ "http://identifiers.org/chebi/CHEBI:42553",
+ "http://identifiers.org/chebi/CHEBI:32966",
+ "http://identifiers.org/chebi/CHEBI:37736",
+ "http://identifiers.org/chebi/CHEBI:28013",
+ "http://identifiers.org/chebi/CHEBI:32967",
+ "http://identifiers.org/chebi/CHEBI:41014",
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},
{
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- "HMDB01311"
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+ "http://identifiers.org/hmdb/HMDB01311",
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},
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},
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+ {
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+ "http://identifiers.org/seed.compound/cpd00003",
+ "http://identifiers.org/unipathway.compound/UPC00003"
+ ]
+ }
+ ]
+ }
},
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"compartment": "c",
"formula": "C21H26N7O14P2",
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},
{
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- "REACT_194697",
- "REACT_29362"
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+ "standardized": {
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+ {
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+ "http://identifiers.org/cas/58-68-4",
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+ "http://identifiers.org/chebi/CHEBI:57945",
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},
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"compartment": "c",
"formula": "C21H27N7O14P2",
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"name": "Nicotinamide adenine dinucleotide - reduced"
},
{
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- "REACT_372364"
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- "unipathway.compound": "UPC00074"
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+ {
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+ }
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},
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"compartment": "c",
"formula": "C3H2O6P",
- "id": "pep_c",
+ "id": "M_pep_c",
"name": "Phosphoenolpyruvate"
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{
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- "cpd09463",
- "cpd00009"
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+ "http://identifiers.org/unipathway.compound/UPC00009"
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+ }
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"compartment": "c",
"formula": "HO4P",
- "id": "pi_c",
+ "id": "M_pi_c",
"name": "Phosphate"
},
{
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- "biocyc": [
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- "PHOSPHATE-GROUP",
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- "CHEBI:39745",
- "CHEBI:24838"
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- "cpd09463",
- "cpd00009"
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+ "standardized": {
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+ "http://identifiers.org/biocyc/PHOSPHATE-GROUP",
+ "http://identifiers.org/biocyc/CPD0-1421",
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+ "http://identifiers.org/unipathway.compound/UPC00009"
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"compartment": "e",
"formula": "HO4P",
- "id": "pi_e",
+ "id": "M_pi_e",
"name": "Phosphate"
},
{
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- "biocyc": "PYRUVATE",
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- "CHEBI:26466",
- "CHEBI:26462"
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- "REACT_389680",
- "REACT_29398"
- ],
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- "unipathway.compound": "UPC00022"
+ "standardized": {
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+ "resources": [
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+ "http://identifiers.org/biocyc/PYRUVATE",
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+ "http://identifiers.org/cas/127-17-3",
+ "http://identifiers.org/chebi/CHEBI:15361",
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+ "http://identifiers.org/seed.compound/cpd00020",
+ "http://identifiers.org/unipathway.compound/UPC00022"
+ ]
+ }
+ ]
+ }
},
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"compartment": "c",
"formula": "C3H3O3",
- "id": "pyr_c",
+ "id": "M_pyr_c",
"name": "Pyruvate"
}
],
"reactions": [
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"annotation": {
- "bigg.reaction": "ATPM"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ATPM"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "",
- "id": "ATPM",
+ "id": "R_ATPM",
"lower_bound": 8.39,
"metabolites": {
- "adp_c": 1.0,
- "atp_c": -1.0,
- "h2o_c": -1.0,
- "h_c": 1.0,
- "pi_c": 1.0
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0,
+ "M_h2o_c": -1.0,
+ "M_h_c": 1.0,
+ "M_pi_c": 1.0
},
"name": "ATP maintenance requirement",
"objective_coefficient": 1.0,
@@ -1126,7 +1201,7 @@
},
{
"gene_reaction_rule": "",
- "id": "D_LACt2",
+ "id": "R_D_LACt2",
"lower_bound": -1000.0,
"metabolites": {},
"name": "",
@@ -1134,148 +1209,218 @@
},
{
"annotation": {
- "bigg.reaction": "ENO"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ENO"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b2779",
- "id": "ENO",
+ "id": "R_ENO",
"lower_bound": -1000.0,
"metabolites": {
- "2pg_c": -1.0,
- "h2o_c": 1.0,
- "pep_c": 1.0
+ "M_2pg_c": -1.0,
+ "M_h2o_c": 1.0,
+ "M_pep_c": 1.0
},
"name": "enolase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "glc",
- "sbo": "SBO:0000627"
+ "sbo": "SBO:0000627",
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/glc"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "",
- "id": "EX_glc__D_e",
+ "id": "R_EX_glc__D_e",
"lower_bound": -10.0,
"metabolites": {
- "glc__D_e": -1.0
+ "M_glc__D_e": -1.0
},
"name": "D-Glucose exchange",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "h",
- "sbo": "SBO:0000627"
+ "sbo": "SBO:0000627",
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/h"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "",
- "id": "EX_h_e",
+ "id": "R_EX_h_e",
"lower_bound": -1000.0,
"metabolites": {
- "h_e": -1.0
+ "M_h_e": -1.0
},
"name": "H+ exchange",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "lac__D",
- "sbo": "SBO:0000627"
+ "sbo": "SBO:0000627",
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/lac__D"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "",
- "id": "EX_lac__D_e",
+ "id": "R_EX_lac__D_e",
"lower_bound": 0.0,
"metabolites": {
- "lac__D_e": -1.0
+ "M_lac__D_e": -1.0
},
"name": "D-lactate exchange",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "FBA"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/FBA"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b1773 or b2097 or b2925",
- "id": "FBA",
+ "id": "R_FBA",
"lower_bound": -1000.0,
"metabolites": {
- "dhap_c": 1.0,
- "fdp_c": -1.0,
- "g3p_c": 1.0
+ "M_dhap_c": 1.0,
+ "M_fdp_c": -1.0,
+ "M_g3p_c": 1.0
},
"name": "fructose-bisphosphate aldolase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "GAPD"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/GAPD"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b1779",
- "id": "GAPD",
+ "id": "R_GAPD",
"lower_bound": -1000.0,
"metabolites": {
- "13dpg_c": 1.0,
- "g3p_c": -1.0,
- "h_c": 1.0,
- "nad_c": -1.0,
- "nadh_c": 1.0,
- "pi_c": -1.0
+ "M_13dpg_c": 1.0,
+ "M_g3p_c": -1.0,
+ "M_h_c": 1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0,
+ "M_pi_c": -1.0
},
"name": "glyceraldehyde-3-phosphate dehydrogenase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "GLCpts"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/GLCpts"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "(b2415 and b2417 and b1101 and b2416) or (b2415 and b2417 and b1621 and b2416) or (b2415 and b1818 and b1817 and b1819 and b2416)",
- "id": "GLCpts",
+ "id": "R_GLCpts",
"lower_bound": 0.0,
"metabolites": {
- "g6p_c": 1.0,
- "glc__D_e": -1.0,
- "pep_c": -1.0,
- "pyr_c": 1.0
+ "M_g6p_c": 1.0,
+ "M_glc__D_e": -1.0,
+ "M_pep_c": -1.0,
+ "M_pyr_c": 1.0
},
"name": "D-glucose transport via PEP:Pyr PTS",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "H2Ot"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/H2Ot"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b0875 or s0001",
- "id": "H2Ot",
+ "id": "R_H2Ot",
"lower_bound": -1000.0,
"metabolites": {
- "h2o_c": 1.0,
- "h2o_e": -1.0
+ "M_h2o_c": 1.0,
+ "M_h2o_e": -1.0
},
"name": "R H2O transport via - diffusion",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "LDH_D",
- "biocyc": "META:DLACTDEHYDROGNAD-RXN",
- "ec-code": "1.1.1.28",
- "kegg.reaction": "R00704",
- "metanetx.reaction": "MNXR101037",
- "rhea": [
- "16369",
- "16370",
- "16371",
- "16372"
- ],
- "sbo": "SBO:0000375"
+ "sbo": "SBO:0000375",
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/LDH_D",
+ "http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN",
+ "http://identifiers.org/ec-code/1.1.1.28",
+ "http://identifiers.org/kegg.reaction/R00704",
+ "http://identifiers.org/metanetx.reaction/MNXR101037",
+ "http://identifiers.org/rhea/16369",
+ "http://identifiers.org/rhea/16370",
+ "http://identifiers.org/rhea/16371",
+ "http://identifiers.org/rhea/16372"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b2133 or b1380",
- "id": "LDH_D",
+ "id": "R_LDH_D",
"lower_bound": -1000.0,
"metabolites": {
- "h_c": 1.0,
- "lac__D_c": -1.0,
- "nad_c": -1.0,
- "nadh_c": 1.0,
- "pyr_c": 1.0
+ "M_h_c": 1.0,
+ "M_lac__D_c": -1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0,
+ "M_pyr_c": 1.0
},
"name": "D-lactate dehydrogenase",
"subsystem": "Pyruvate Metabolism",
@@ -1283,17 +1428,25 @@
},
{
"annotation": {
- "bigg.reaction": "PFK"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PFK"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b3916 or b1723",
- "id": "PFK",
+ "id": "R_PFK",
"lower_bound": 0.0,
"metabolites": {
- "adp_c": 1.0,
- "atp_c": -1.0,
- "f6p_c": -1.0,
- "fdp_c": 1.0,
- "h_c": 1.0
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0,
+ "M_f6p_c": -1.0,
+ "M_fdp_c": 1.0,
+ "M_h_c": 1.0
},
"name": "phosphofructokinase",
"objective_coefficient": 1.0,
@@ -1301,91 +1454,139 @@
},
{
"annotation": {
- "bigg.reaction": "PGI"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGI"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b4025",
- "id": "PGI",
+ "id": "R_PGI",
"lower_bound": -1000.0,
"metabolites": {
- "f6p_c": 1.0,
- "g6p_c": -1.0
+ "M_f6p_c": 1.0,
+ "M_g6p_c": -1.0
},
"name": "glucose-6-phosphate isomerase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "PGK"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGK"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b2926",
- "id": "PGK",
+ "id": "R_PGK",
"lower_bound": -1000.0,
"metabolites": {
- "13dpg_c": 1.0,
- "3pg_c": -1.0,
- "adp_c": 1.0,
- "atp_c": -1.0
+ "M_13dpg_c": 1.0,
+ "M_3pg_c": -1.0,
+ "M_adp_c": 1.0,
+ "M_atp_c": -1.0
},
"name": "phosphoglycerate kinase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "PGM"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PGM"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b4395 or b3612 or b0755",
- "id": "PGM",
+ "id": "R_PGM",
"lower_bound": -1000.0,
"metabolites": {
- "2pg_c": -1.0,
- "3pg_c": 1.0
+ "M_2pg_c": -1.0,
+ "M_3pg_c": 1.0
},
"name": "phosphoglycerate mutase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "PIt2r"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PIt2r"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b2987 or b3493",
- "id": "PIt2r",
+ "id": "R_PIt2r",
"lower_bound": -1000.0,
"metabolites": {
- "h_c": 1.0,
- "h_e": -1.0,
- "pi_c": 1.0,
- "pi_e": -1.0
+ "M_h_c": 1.0,
+ "M_h_e": -1.0,
+ "M_pi_c": 1.0,
+ "M_pi_e": -1.0
},
"name": "R phosphate reversible transport via - symport",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "PYK"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/PYK"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b1854 or b1676",
- "id": "PYK",
+ "id": "R_PYK",
"lower_bound": 0.0,
"metabolites": {
- "adp_c": -1.0,
- "atp_c": 1.0,
- "h_c": -1.0,
- "pep_c": -1.0,
- "pyr_c": 1.0
+ "M_adp_c": -1.0,
+ "M_atp_c": 1.0,
+ "M_h_c": -1.0,
+ "M_pep_c": -1.0,
+ "M_pyr_c": 1.0
},
"name": "pyruvate kinase",
"upper_bound": 1000.0
},
{
"annotation": {
- "bigg.reaction": "TPI"
+ "standardized": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/TPI"
+ ]
+ }
+ ]
+ }
},
"gene_reaction_rule": "b3919",
- "id": "TPI",
+ "id": "R_TPI",
"lower_bound": -1000.0,
"metabolites": {
- "dhap_c": -1.0,
- "g3p_c": 1.0
+ "M_dhap_c": -1.0,
+ "M_g3p_c": 1.0
},
"name": "triose-phosphate isomerase",
"upper_bound": 1000.0
diff --git a/src/cobra/data/mini.mat b/src/cobra/data/mini.mat
index 9f46abd4c..6f3a67bdc 100644
Binary files a/src/cobra/data/mini.mat and b/src/cobra/data/mini.mat differ
diff --git a/src/cobra/data/mini.pickle b/src/cobra/data/mini.pickle
index b0e0f1f40..864117c30 100644
Binary files a/src/cobra/data/mini.pickle and b/src/cobra/data/mini.pickle differ
diff --git a/src/cobra/data/mini.yml b/src/cobra/data/mini.yml
index cd9a28a41..6f75b9cf6 100644
--- a/src/cobra/data/mini.yml
+++ b/src/cobra/data/mini.yml
@@ -1,1168 +1,1233 @@
!!omap
- metabolites:
- !!omap
- - id: 13dpg_c
+ - id: M_13dpg_c
- name: 3-Phospho-D-glyceroyl phosphate
- compartment: c
- charge: -4
- formula: C3H4O10P2
- annotation: !!omap
- - bigg.metabolite: 13dpg
- - biocyc: DPG
- - chebi:
- - CHEBI:16001
- - CHEBI:1658
- - CHEBI:20189
- - CHEBI:57604
- - CHEBI:11881
- - hmdb: HMDB01270
- - kegg.compound: C00236
- - pubchem.substance: '3535'
- - reactome: REACT_29800
- - seed.compound: cpd00203
- - unipathway.compound: UPC00236
- - !!omap
- - id: 2pg_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/13dpg
+ - http://identifiers.org/biocyc/DPG
+ - http://identifiers.org/chebi/CHEBI:16001
+ - http://identifiers.org/chebi/CHEBI:1658
+ - http://identifiers.org/chebi/CHEBI:20189
+ - http://identifiers.org/chebi/CHEBI:57604
+ - http://identifiers.org/chebi/CHEBI:11881
+ - http://identifiers.org/hmdb/HMDB01270
+ - http://identifiers.org/kegg.compound/C00236
+ - http://identifiers.org/pubchem.substance/3535
+ - http://identifiers.org/reactome/REACT_29800
+ - http://identifiers.org/seed.compound/cpd00203
+ - http://identifiers.org/unipathway.compound/UPC00236
+ - !!omap
+ - id: M_2pg_c
- name: D-Glycerate 2-phosphate
- compartment: c
- charge: -3
- formula: C3H4O7P
- annotation: !!omap
- - bigg.metabolite: 2pg
- - biocyc: 2-PG
- - chebi:
- - CHEBI:1267
- - CHEBI:58289
- - CHEBI:17835
- - CHEBI:21028
- - CHEBI:11651
- - CHEBI:12986
- - CHEBI:24344
- - CHEBI:39868
- - hmdb:
- - HMDB03391
- - HMDB00362
- - kegg.compound: C00631
- - pubchem.substance: '3904'
- - reactome: REACT_30485
- - seed.compound: cpd00482
- - unipathway.compound: UPC00631
- - !!omap
- - id: 3pg_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/2pg
+ - http://identifiers.org/biocyc/2-PG
+ - http://identifiers.org/chebi/CHEBI:1267
+ - http://identifiers.org/chebi/CHEBI:58289
+ - http://identifiers.org/chebi/CHEBI:17835
+ - http://identifiers.org/chebi/CHEBI:21028
+ - http://identifiers.org/chebi/CHEBI:11651
+ - http://identifiers.org/chebi/CHEBI:12986
+ - http://identifiers.org/chebi/CHEBI:24344
+ - http://identifiers.org/chebi/CHEBI:39868
+ - http://identifiers.org/hmdb/HMDB03391
+ - http://identifiers.org/hmdb/HMDB00362
+ - http://identifiers.org/kegg.compound/C00631
+ - http://identifiers.org/pubchem.substance/3904
+ - http://identifiers.org/reactome/REACT_30485
+ - http://identifiers.org/seed.compound/cpd00482
+ - http://identifiers.org/unipathway.compound/UPC00631
+ - !!omap
+ - id: M_3pg_c
- name: 3-Phospho-D-glycerate
- compartment: c
- charge: -3
- formula: C3H4O7P
- annotation: !!omap
- - bigg.metabolite: 3pg
- - biocyc: G3P
- - chebi:
- - CHEBI:40016
- - CHEBI:58272
- - CHEBI:57998
- - CHEBI:11879
- - CHEBI:1657
- - CHEBI:1659
- - CHEBI:17050
- - CHEBI:21029
- - CHEBI:11882
- - CHEBI:11880
- - CHEBI:12987
- - CHEBI:17794
- - CHEBI:24345
- - hmdb: HMDB00807
- - kegg.compound:
- - C00197
- - C00597
- - pubchem.substance: '3497'
- - reactome: REACT_29728
- - seed.compound: cpd00169
- - unipathway.compound:
- - UPC00597
- - UPC00197
- - !!omap
- - id: adp_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/3pg
+ - http://identifiers.org/biocyc/G3P
+ - http://identifiers.org/chebi/CHEBI:40016
+ - http://identifiers.org/chebi/CHEBI:58272
+ - http://identifiers.org/chebi/CHEBI:57998
+ - http://identifiers.org/chebi/CHEBI:11879
+ - http://identifiers.org/chebi/CHEBI:1657
+ - http://identifiers.org/chebi/CHEBI:1659
+ - http://identifiers.org/chebi/CHEBI:17050
+ - http://identifiers.org/chebi/CHEBI:21029
+ - http://identifiers.org/chebi/CHEBI:11882
+ - http://identifiers.org/chebi/CHEBI:11880
+ - http://identifiers.org/chebi/CHEBI:12987
+ - http://identifiers.org/chebi/CHEBI:17794
+ - http://identifiers.org/chebi/CHEBI:24345
+ - http://identifiers.org/hmdb/HMDB00807
+ - http://identifiers.org/kegg.compound/C00197
+ - http://identifiers.org/kegg.compound/C00597
+ - http://identifiers.org/pubchem.substance/3497
+ - http://identifiers.org/reactome/REACT_29728
+ - http://identifiers.org/seed.compound/cpd00169
+ - http://identifiers.org/unipathway.compound/UPC00597
+ - http://identifiers.org/unipathway.compound/UPC00197
+ - !!omap
+ - id: M_adp_c
- name: ADP
- compartment: c
- charge: -3
- formula: C10H12N5O10P2
- annotation: !!omap
- - bigg.metabolite: adp
- - biocyc:
- - ADP
- - ADP-GROUP
- - cas:
- - 58-64-0
- - chebi:
- - CHEBI:13222
- - CHEBI:16761
- - CHEBI:2342
- - CHEBI:22244
- - CHEBI:40553
- - CHEBI:456216
- - hmdb: HMDB01341
- - kegg.compound: C00008
- - kegg.glycan: G11113
- - pubchem.substance: '3310'
- - reactome:
- - REACT_190072
- - REACT_481002
- - REACT_211606
- - REACT_429160
- - REACT_29370
- - REACT_196180
- - REACT_113581
- - REACT_113582
- - REACT_114564
- - REACT_114565
- - REACT_429153
- - seed.compound: cpd00008
- - unipathway.compound: UPC00008
- - !!omap
- - id: atp_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/adp
+ - http://identifiers.org/biocyc/ADP
+ - http://identifiers.org/biocyc/ADP-GROUP
+ - http://identifiers.org/cas/58-64-0
+ - http://identifiers.org/cas/58-64-0
+ - http://identifiers.org/chebi/CHEBI:13222
+ - http://identifiers.org/chebi/CHEBI:16761
+ - http://identifiers.org/chebi/CHEBI:2342
+ - http://identifiers.org/chebi/CHEBI:22244
+ - http://identifiers.org/chebi/CHEBI:40553
+ - http://identifiers.org/chebi/CHEBI:456216
+ - http://identifiers.org/hmdb/HMDB01341
+ - http://identifiers.org/kegg.compound/C00008
+ - http://identifiers.org/kegg.glycan/G11113
+ - http://identifiers.org/pubchem.substance/3310
+ - http://identifiers.org/reactome/REACT_190072
+ - http://identifiers.org/reactome/REACT_481002
+ - http://identifiers.org/reactome/REACT_211606
+ - http://identifiers.org/reactome/REACT_429160
+ - http://identifiers.org/reactome/REACT_29370
+ - http://identifiers.org/reactome/REACT_196180
+ - http://identifiers.org/reactome/REACT_113581
+ - http://identifiers.org/reactome/REACT_113582
+ - http://identifiers.org/reactome/REACT_114564
+ - http://identifiers.org/reactome/REACT_114565
+ - http://identifiers.org/reactome/REACT_429153
+ - http://identifiers.org/seed.compound/cpd00008
+ - http://identifiers.org/unipathway.compound/UPC00008
+ - !!omap
+ - id: M_atp_c
- name: ATP
- compartment: c
- charge: -4
- formula: C10H12N5O13P3
- annotation: !!omap
- - bigg.metabolite: atp
- - biocyc: ATP
- - cas:
- - 56-65-5
- - chebi:
- - CHEBI:40938
- - CHEBI:15422
- - CHEBI:57299
- - CHEBI:13236
- - CHEBI:10789
- - CHEBI:30616
- - CHEBI:22249
- - CHEBI:10841
- - CHEBI:2359
- - hmdb: HMDB00538
- - kegg.compound: C00002
- - kegg.drug: D08646
- - pubchem.substance: '3304'
- - reactome:
- - REACT_190078
- - REACT_113592
- - REACT_113593
- - REACT_114570
- - REACT_29358
- - REACT_389573
- - REACT_139836
- - REACT_211579
- - seed.compound: cpd00002
- - unipathway.compound: UPC00002
- - !!omap
- - id: dhap_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/atp
+ - http://identifiers.org/biocyc/ATP
+ - http://identifiers.org/cas/56-65-5
+ - http://identifiers.org/cas/56-65-5
+ - http://identifiers.org/chebi/CHEBI:40938
+ - http://identifiers.org/chebi/CHEBI:15422
+ - http://identifiers.org/chebi/CHEBI:57299
+ - http://identifiers.org/chebi/CHEBI:13236
+ - http://identifiers.org/chebi/CHEBI:10789
+ - http://identifiers.org/chebi/CHEBI:30616
+ - http://identifiers.org/chebi/CHEBI:22249
+ - http://identifiers.org/chebi/CHEBI:10841
+ - http://identifiers.org/chebi/CHEBI:2359
+ - http://identifiers.org/hmdb/HMDB00538
+ - http://identifiers.org/kegg.compound/C00002
+ - http://identifiers.org/kegg.drug/D08646
+ - http://identifiers.org/pubchem.substance/3304
+ - http://identifiers.org/reactome/REACT_190078
+ - http://identifiers.org/reactome/REACT_113592
+ - http://identifiers.org/reactome/REACT_113593
+ - http://identifiers.org/reactome/REACT_114570
+ - http://identifiers.org/reactome/REACT_29358
+ - http://identifiers.org/reactome/REACT_389573
+ - http://identifiers.org/reactome/REACT_139836
+ - http://identifiers.org/reactome/REACT_211579
+ - http://identifiers.org/seed.compound/cpd00002
+ - http://identifiers.org/unipathway.compound/UPC00002
+ - !!omap
+ - id: M_dhap_c
- name: Dihydroxyacetone phosphate
- compartment: c
- charge: -2
- formula: C3H5O6P
- annotation: !!omap
- - bigg.metabolite: dhap
- - biocyc: DIHYDROXY-ACETONE-PHOSPHATE
- - cas:
- - 57-04-5
- - chebi:
- - CHEBI:14341
- - CHEBI:57642
- - CHEBI:14342
- - CHEBI:16108
- - CHEBI:5454
- - CHEBI:24355
- - CHEBI:39571
- - hmdb:
- - HMDB01473
- - HMDB11735
- - kegg.compound: C00111
- - pubchem.substance: '3411'
- - reactome:
- - REACT_188451
- - REACT_75970
- - REACT_390404
- - seed.compound: cpd00095
- - unipathway.compound: UPC00111
- - !!omap
- - id: f6p_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/dhap
+ - http://identifiers.org/biocyc/DIHYDROXY-ACETONE-PHOSPHATE
+ - http://identifiers.org/cas/57-04-5
+ - http://identifiers.org/cas/57-04-5
+ - http://identifiers.org/chebi/CHEBI:14341
+ - http://identifiers.org/chebi/CHEBI:57642
+ - http://identifiers.org/chebi/CHEBI:14342
+ - http://identifiers.org/chebi/CHEBI:16108
+ - http://identifiers.org/chebi/CHEBI:5454
+ - http://identifiers.org/chebi/CHEBI:24355
+ - http://identifiers.org/chebi/CHEBI:39571
+ - http://identifiers.org/hmdb/HMDB01473
+ - http://identifiers.org/hmdb/HMDB11735
+ - http://identifiers.org/kegg.compound/C00111
+ - http://identifiers.org/pubchem.substance/3411
+ - http://identifiers.org/reactome/REACT_188451
+ - http://identifiers.org/reactome/REACT_75970
+ - http://identifiers.org/reactome/REACT_390404
+ - http://identifiers.org/seed.compound/cpd00095
+ - http://identifiers.org/unipathway.compound/UPC00111
+ - !!omap
+ - id: M_f6p_c
- name: D-Fructose 6-phosphate
- compartment: c
- charge: -2
- formula: C6H11O9P
- annotation: !!omap
- - bigg.metabolite: f6p
- - biocyc: FRUCTOSE-6P
- - cas:
- - 643-13-0
- - chebi:
- - CHEBI:57634
- - CHEBI:12352
- - CHEBI:45804
- - CHEBI:61527
- - CHEBI:61553
- - CHEBI:10375
- - CHEBI:16084
- - CHEBI:42378
- - CHEBI:22768
- - hmdb: HMDB03971
- - kegg.compound:
- - C05345
- - C00085
- - pubchem.substance: '3385'
- - seed.compound: cpd00072
- - unipathway.compound:
- - UPC05345
- - UPC00085
- - !!omap
- - id: fdp_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/f6p
+ - http://identifiers.org/biocyc/FRUCTOSE-6P
+ - http://identifiers.org/cas/643-13-0
+ - http://identifiers.org/cas/643-13-0
+ - http://identifiers.org/chebi/CHEBI:57634
+ - http://identifiers.org/chebi/CHEBI:12352
+ - http://identifiers.org/chebi/CHEBI:45804
+ - http://identifiers.org/chebi/CHEBI:61527
+ - http://identifiers.org/chebi/CHEBI:61553
+ - http://identifiers.org/chebi/CHEBI:10375
+ - http://identifiers.org/chebi/CHEBI:16084
+ - http://identifiers.org/chebi/CHEBI:42378
+ - http://identifiers.org/chebi/CHEBI:22768
+ - http://identifiers.org/hmdb/HMDB03971
+ - http://identifiers.org/kegg.compound/C05345
+ - http://identifiers.org/kegg.compound/C00085
+ - http://identifiers.org/pubchem.substance/3385
+ - http://identifiers.org/seed.compound/cpd00072
+ - http://identifiers.org/unipathway.compound/UPC05345
+ - http://identifiers.org/unipathway.compound/UPC00085
+ - !!omap
+ - id: M_fdp_c
- name: D-Fructose 1,6-bisphosphate
- compartment: c
- charge: -4
- formula: C6H10O12P2
- annotation: !!omap
- - bigg.metabolite: fdp
- - biocyc: FRUCTOSE-16-DIPHOSPHATE
- - cas:
- - 488-69-7
- - chebi:
- - CHEBI:32968
- - CHEBI:49299
- - CHEBI:42553
- - CHEBI:32966
- - CHEBI:37736
- - CHEBI:28013
- - CHEBI:32967
- - CHEBI:41014
- - CHEBI:22767
- - CHEBI:10374
- - CHEBI:40595
- - CHEBI:40591
- - kegg.compound:
- - C05378
- - C00354
- - pubchem.substance: '3647'
- - seed.compound: cpd00290
- - unipathway.compound: UPC00354
- - !!omap
- - id: g3p_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/fdp
+ - http://identifiers.org/biocyc/FRUCTOSE-16-DIPHOSPHATE
+ - http://identifiers.org/cas/488-69-7
+ - http://identifiers.org/cas/488-69-7
+ - http://identifiers.org/chebi/CHEBI:32968
+ - http://identifiers.org/chebi/CHEBI:49299
+ - http://identifiers.org/chebi/CHEBI:42553
+ - http://identifiers.org/chebi/CHEBI:32966
+ - http://identifiers.org/chebi/CHEBI:37736
+ - http://identifiers.org/chebi/CHEBI:28013
+ - http://identifiers.org/chebi/CHEBI:32967
+ - http://identifiers.org/chebi/CHEBI:41014
+ - http://identifiers.org/chebi/CHEBI:22767
+ - http://identifiers.org/chebi/CHEBI:10374
+ - http://identifiers.org/chebi/CHEBI:40595
+ - http://identifiers.org/chebi/CHEBI:40591
+ - http://identifiers.org/kegg.compound/C05378
+ - http://identifiers.org/kegg.compound/C00354
+ - http://identifiers.org/pubchem.substance/3647
+ - http://identifiers.org/seed.compound/cpd00290
+ - http://identifiers.org/unipathway.compound/UPC00354
+ - !!omap
+ - id: M_g3p_c
- name: Glyceraldehyde 3-phosphate
- compartment: c
- charge: -2
- formula: C3H5O6P
- annotation: !!omap
- - bigg.metabolite: g3p
- - cas:
- - 142-10-9
- - chebi:
- - CHEBI:17138
- - CHEBI:14333
- - CHEBI:5446
- - CHEBI:58027
- - hmdb: HMDB01112
- - kegg.compound:
- - C00661
- - C00118
- - pubchem.substance: '3930'
- - seed.compound: cpd00102
- - unipathway.compound:
- - UPC00661
- - UPC00118
- - !!omap
- - id: g6p_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/g3p
+ - http://identifiers.org/cas/142-10-9
+ - http://identifiers.org/cas/142-10-9
+ - http://identifiers.org/chebi/CHEBI:17138
+ - http://identifiers.org/chebi/CHEBI:14333
+ - http://identifiers.org/chebi/CHEBI:5446
+ - http://identifiers.org/chebi/CHEBI:58027
+ - http://identifiers.org/hmdb/HMDB01112
+ - http://identifiers.org/kegg.compound/C00661
+ - http://identifiers.org/kegg.compound/C00118
+ - http://identifiers.org/pubchem.substance/3930
+ - http://identifiers.org/seed.compound/cpd00102
+ - http://identifiers.org/unipathway.compound/UPC00661
+ - http://identifiers.org/unipathway.compound/UPC00118
+ - !!omap
+ - id: M_g6p_c
- name: D-Glucose 6-phosphate
- compartment: c
- charge: -2
- formula: C6H11O9P
- annotation: !!omap
- - bigg.metabolite: g6p
- - biocyc:
- - D-glucose-6-phosphate
- - GLC-6-P
- - cas:
- - 56-73-5
- - chebi:
- - CHEBI:10399
- - CHEBI:22797
- - CHEBI:41041
- - CHEBI:17719
- - CHEBI:4170
- - CHEBI:61548
- - CHEBI:58247
- - CHEBI:12375
- - hmdb:
- - HMDB03498
- - HMDB06793
- - HMDB01401
- - HMDB01549
- - kegg.compound:
- - C00092
- - C01172
- - pubchem.substance: '3392'
- - reactome: REACT_1629756
- - seed.compound: cpd00079
- - unipathway.compound: UPC00092
- - !!omap
- - id: glc__D_e
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/g6p
+ - http://identifiers.org/biocyc/D-glucose-6-phosphate
+ - http://identifiers.org/biocyc/GLC-6-P
+ - http://identifiers.org/cas/56-73-5
+ - http://identifiers.org/cas/56-73-5
+ - http://identifiers.org/chebi/CHEBI:10399
+ - http://identifiers.org/chebi/CHEBI:22797
+ - http://identifiers.org/chebi/CHEBI:41041
+ - http://identifiers.org/chebi/CHEBI:17719
+ - http://identifiers.org/chebi/CHEBI:4170
+ - http://identifiers.org/chebi/CHEBI:61548
+ - http://identifiers.org/chebi/CHEBI:58247
+ - http://identifiers.org/chebi/CHEBI:12375
+ - http://identifiers.org/hmdb/HMDB03498
+ - http://identifiers.org/hmdb/HMDB06793
+ - http://identifiers.org/hmdb/HMDB01401
+ - http://identifiers.org/hmdb/HMDB01549
+ - http://identifiers.org/kegg.compound/C00092
+ - http://identifiers.org/kegg.compound/C01172
+ - http://identifiers.org/pubchem.substance/3392
+ - http://identifiers.org/reactome/REACT_1629756
+ - http://identifiers.org/seed.compound/cpd00079
+ - http://identifiers.org/unipathway.compound/UPC00092
+ - !!omap
+ - id: M_glc__D_e
- name: D-Glucose
- compartment: e
- charge: 0
- formula: C6H12O6
- annotation: !!omap
- - bigg.metabolite: glc__D
- - cas:
- - 50-99-7
- - kegg.compound: C00031
- - pubchem.substance: '3333'
- - !!omap
- - id: h2o_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/glc__D
+ - http://identifiers.org/cas/50-99-7
+ - http://identifiers.org/cas/50-99-7
+ - http://identifiers.org/kegg.compound/C00031
+ - http://identifiers.org/pubchem.substance/3333
+ - !!omap
+ - id: M_h2o_c
- name: H2O
- compartment: c
- charge: 0
- formula: H2O
- annotation: !!omap
- - bigg.metabolite: h2o
- - biocyc:
- - WATER
- - OH
- - OXONIUM
- - cas:
- - 7732-18-5
- - chebi:
- - CHEBI:15377
- - CHEBI:13365
- - CHEBI:41979
- - CHEBI:16234
- - CHEBI:36385
- - CHEBI:42857
- - CHEBI:27313
- - CHEBI:44819
- - CHEBI:29373
- - CHEBI:10743
- - CHEBI:5594
- - CHEBI:29356
- - CHEBI:53442
- - CHEBI:29375
- - CHEBI:29374
- - CHEBI:13419
- - CHEBI:43228
- - CHEBI:44292
- - CHEBI:13352
- - CHEBI:41981
- - CHEBI:29412
- - CHEBI:42043
- - CHEBI:33811
- - CHEBI:33813
- - CHEBI:35511
- - CHEBI:5585
- - CHEBI:44641
- - CHEBI:44701
- - hmdb:
- - HMDB01039
- - HMDB02111
- - kegg.compound:
- - C01328
- - C00001
- - C18714
- - C18712
- - kegg.drug:
- - D00001
- - D06322
- - D03703
- - pubchem.substance: '3303'
- - reactome:
- - REACT_947593
- - REACT_189422
- - REACT_141343
- - REACT_113518
- - REACT_1605715
- - REACT_109276
- - REACT_113521
- - REACT_113519
- - REACT_2022884
- - REACT_351603
- - REACT_29356
- - seed.compound:
- - cpd15275
- - cpd00001
- - unipathway.compound:
- - UPC00001
- - UPC01328
- - !!omap
- - id: h2o_e
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/h2o
+ - http://identifiers.org/biocyc/WATER
+ - http://identifiers.org/biocyc/OH
+ - http://identifiers.org/biocyc/OXONIUM
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/chebi/CHEBI:15377
+ - http://identifiers.org/chebi/CHEBI:13365
+ - http://identifiers.org/chebi/CHEBI:41979
+ - http://identifiers.org/chebi/CHEBI:16234
+ - http://identifiers.org/chebi/CHEBI:36385
+ - http://identifiers.org/chebi/CHEBI:42857
+ - http://identifiers.org/chebi/CHEBI:27313
+ - http://identifiers.org/chebi/CHEBI:44819
+ - http://identifiers.org/chebi/CHEBI:29373
+ - http://identifiers.org/chebi/CHEBI:10743
+ - http://identifiers.org/chebi/CHEBI:5594
+ - http://identifiers.org/chebi/CHEBI:29356
+ - http://identifiers.org/chebi/CHEBI:53442
+ - http://identifiers.org/chebi/CHEBI:29375
+ - http://identifiers.org/chebi/CHEBI:29374
+ - http://identifiers.org/chebi/CHEBI:13419
+ - http://identifiers.org/chebi/CHEBI:43228
+ - http://identifiers.org/chebi/CHEBI:44292
+ - http://identifiers.org/chebi/CHEBI:13352
+ - http://identifiers.org/chebi/CHEBI:41981
+ - http://identifiers.org/chebi/CHEBI:29412
+ - http://identifiers.org/chebi/CHEBI:42043
+ - http://identifiers.org/chebi/CHEBI:33811
+ - http://identifiers.org/chebi/CHEBI:33813
+ - http://identifiers.org/chebi/CHEBI:35511
+ - http://identifiers.org/chebi/CHEBI:5585
+ - http://identifiers.org/chebi/CHEBI:44641
+ - http://identifiers.org/chebi/CHEBI:44701
+ - http://identifiers.org/hmdb/HMDB01039
+ - http://identifiers.org/hmdb/HMDB02111
+ - http://identifiers.org/kegg.compound/C01328
+ - http://identifiers.org/kegg.compound/C00001
+ - http://identifiers.org/kegg.compound/C18714
+ - http://identifiers.org/kegg.compound/C18712
+ - http://identifiers.org/kegg.drug/D00001
+ - http://identifiers.org/kegg.drug/D06322
+ - http://identifiers.org/kegg.drug/D03703
+ - http://identifiers.org/pubchem.substance/3303
+ - http://identifiers.org/reactome/REACT_947593
+ - http://identifiers.org/reactome/REACT_189422
+ - http://identifiers.org/reactome/REACT_141343
+ - http://identifiers.org/reactome/REACT_113518
+ - http://identifiers.org/reactome/REACT_1605715
+ - http://identifiers.org/reactome/REACT_109276
+ - http://identifiers.org/reactome/REACT_113521
+ - http://identifiers.org/reactome/REACT_113519
+ - http://identifiers.org/reactome/REACT_2022884
+ - http://identifiers.org/reactome/REACT_351603
+ - http://identifiers.org/reactome/REACT_29356
+ - http://identifiers.org/seed.compound/cpd15275
+ - http://identifiers.org/seed.compound/cpd00001
+ - http://identifiers.org/unipathway.compound/UPC00001
+ - http://identifiers.org/unipathway.compound/UPC01328
+ - !!omap
+ - id: M_h2o_e
- name: H2O
- compartment: e
- charge: 0
- formula: H2O
- annotation: !!omap
- - bigg.metabolite: h2o
- - biocyc:
- - WATER
- - OH
- - OXONIUM
- - cas:
- - 7732-18-5
- - chebi:
- - CHEBI:15377
- - CHEBI:13365
- - CHEBI:41979
- - CHEBI:16234
- - CHEBI:36385
- - CHEBI:42857
- - CHEBI:27313
- - CHEBI:44819
- - CHEBI:29373
- - CHEBI:10743
- - CHEBI:5594
- - CHEBI:29356
- - CHEBI:53442
- - CHEBI:29375
- - CHEBI:29374
- - CHEBI:13419
- - CHEBI:43228
- - CHEBI:44292
- - CHEBI:13352
- - CHEBI:41981
- - CHEBI:29412
- - CHEBI:42043
- - CHEBI:33811
- - CHEBI:33813
- - CHEBI:35511
- - CHEBI:5585
- - CHEBI:44641
- - CHEBI:44701
- - hmdb:
- - HMDB01039
- - HMDB02111
- - kegg.compound:
- - C01328
- - C00001
- - C18714
- - C18712
- - kegg.drug:
- - D00001
- - D06322
- - D03703
- - pubchem.substance: '3303'
- - reactome:
- - REACT_947593
- - REACT_189422
- - REACT_141343
- - REACT_113518
- - REACT_1605715
- - REACT_109276
- - REACT_113521
- - REACT_113519
- - REACT_2022884
- - REACT_351603
- - REACT_29356
- - seed.compound:
- - cpd15275
- - cpd00001
- - unipathway.compound:
- - UPC00001
- - UPC01328
- - !!omap
- - id: h_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/h2o
+ - http://identifiers.org/biocyc/WATER
+ - http://identifiers.org/biocyc/OH
+ - http://identifiers.org/biocyc/OXONIUM
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/cas/7732-18-5
+ - http://identifiers.org/chebi/CHEBI:15377
+ - http://identifiers.org/chebi/CHEBI:13365
+ - http://identifiers.org/chebi/CHEBI:41979
+ - http://identifiers.org/chebi/CHEBI:16234
+ - http://identifiers.org/chebi/CHEBI:36385
+ - http://identifiers.org/chebi/CHEBI:42857
+ - http://identifiers.org/chebi/CHEBI:27313
+ - http://identifiers.org/chebi/CHEBI:44819
+ - http://identifiers.org/chebi/CHEBI:29373
+ - http://identifiers.org/chebi/CHEBI:10743
+ - http://identifiers.org/chebi/CHEBI:5594
+ - http://identifiers.org/chebi/CHEBI:29356
+ - http://identifiers.org/chebi/CHEBI:53442
+ - http://identifiers.org/chebi/CHEBI:29375
+ - http://identifiers.org/chebi/CHEBI:29374
+ - http://identifiers.org/chebi/CHEBI:13419
+ - http://identifiers.org/chebi/CHEBI:43228
+ - http://identifiers.org/chebi/CHEBI:44292
+ - http://identifiers.org/chebi/CHEBI:13352
+ - http://identifiers.org/chebi/CHEBI:41981
+ - http://identifiers.org/chebi/CHEBI:29412
+ - http://identifiers.org/chebi/CHEBI:42043
+ - http://identifiers.org/chebi/CHEBI:33811
+ - http://identifiers.org/chebi/CHEBI:33813
+ - http://identifiers.org/chebi/CHEBI:35511
+ - http://identifiers.org/chebi/CHEBI:5585
+ - http://identifiers.org/chebi/CHEBI:44641
+ - http://identifiers.org/chebi/CHEBI:44701
+ - http://identifiers.org/hmdb/HMDB01039
+ - http://identifiers.org/hmdb/HMDB02111
+ - http://identifiers.org/kegg.compound/C01328
+ - http://identifiers.org/kegg.compound/C00001
+ - http://identifiers.org/kegg.compound/C18714
+ - http://identifiers.org/kegg.compound/C18712
+ - http://identifiers.org/kegg.drug/D00001
+ - http://identifiers.org/kegg.drug/D06322
+ - http://identifiers.org/kegg.drug/D03703
+ - http://identifiers.org/pubchem.substance/3303
+ - http://identifiers.org/reactome/REACT_947593
+ - http://identifiers.org/reactome/REACT_189422
+ - http://identifiers.org/reactome/REACT_141343
+ - http://identifiers.org/reactome/REACT_113518
+ - http://identifiers.org/reactome/REACT_1605715
+ - http://identifiers.org/reactome/REACT_109276
+ - http://identifiers.org/reactome/REACT_113521
+ - http://identifiers.org/reactome/REACT_113519
+ - http://identifiers.org/reactome/REACT_2022884
+ - http://identifiers.org/reactome/REACT_351603
+ - http://identifiers.org/reactome/REACT_29356
+ - http://identifiers.org/seed.compound/cpd15275
+ - http://identifiers.org/seed.compound/cpd00001
+ - http://identifiers.org/unipathway.compound/UPC00001
+ - http://identifiers.org/unipathway.compound/UPC01328
+ - !!omap
+ - id: M_h_c
- name: H+
- compartment: c
- charge: 1
- formula: H
- annotation: !!omap
- - bigg.metabolite: h
- - biocyc: PROTON
- - cas:
- - 12408-02-5
- - chebi:
- - CHEBI:24636
- - CHEBI:15378
- - CHEBI:10744
- - CHEBI:13357
- - CHEBI:5584
- - kegg.compound: C00080
- - pubchem.substance: '3380'
- - reactome:
- - REACT_194688
- - REACT_425978
- - REACT_193465
- - REACT_374900
- - REACT_74722
- - REACT_425999
- - REACT_428040
- - REACT_163953
- - REACT_372511
- - REACT_2000349
- - REACT_70106
- - REACT_1470067
- - REACT_113529
- - REACT_425969
- - REACT_428548
- - REACT_156540
- - REACT_1614597
- - REACT_351626
- - REACT_427899
- - seed.compound: cpd00067
- - unipathway.compound: UPC00080
- - !!omap
- - id: h_e
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/h
+ - http://identifiers.org/biocyc/PROTON
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/chebi/CHEBI:24636
+ - http://identifiers.org/chebi/CHEBI:15378
+ - http://identifiers.org/chebi/CHEBI:10744
+ - http://identifiers.org/chebi/CHEBI:13357
+ - http://identifiers.org/chebi/CHEBI:5584
+ - http://identifiers.org/kegg.compound/C00080
+ - http://identifiers.org/pubchem.substance/3380
+ - http://identifiers.org/reactome/REACT_194688
+ - http://identifiers.org/reactome/REACT_425978
+ - http://identifiers.org/reactome/REACT_193465
+ - http://identifiers.org/reactome/REACT_374900
+ - http://identifiers.org/reactome/REACT_74722
+ - http://identifiers.org/reactome/REACT_425999
+ - http://identifiers.org/reactome/REACT_428040
+ - http://identifiers.org/reactome/REACT_163953
+ - http://identifiers.org/reactome/REACT_372511
+ - http://identifiers.org/reactome/REACT_2000349
+ - http://identifiers.org/reactome/REACT_70106
+ - http://identifiers.org/reactome/REACT_1470067
+ - http://identifiers.org/reactome/REACT_113529
+ - http://identifiers.org/reactome/REACT_425969
+ - http://identifiers.org/reactome/REACT_428548
+ - http://identifiers.org/reactome/REACT_156540
+ - http://identifiers.org/reactome/REACT_1614597
+ - http://identifiers.org/reactome/REACT_351626
+ - http://identifiers.org/reactome/REACT_427899
+ - http://identifiers.org/seed.compound/cpd00067
+ - http://identifiers.org/unipathway.compound/UPC00080
+ - !!omap
+ - id: M_h_e
- name: H+
- compartment: e
- charge: 1
- formula: H
- annotation: !!omap
- - bigg.metabolite: h
- - biocyc: PROTON
- - cas:
- - 12408-02-5
- - chebi:
- - CHEBI:24636
- - CHEBI:15378
- - CHEBI:10744
- - CHEBI:13357
- - CHEBI:5584
- - kegg.compound: C00080
- - pubchem.substance: '3380'
- - reactome:
- - REACT_194688
- - REACT_425978
- - REACT_193465
- - REACT_374900
- - REACT_74722
- - REACT_425999
- - REACT_428040
- - REACT_163953
- - REACT_372511
- - REACT_2000349
- - REACT_70106
- - REACT_1470067
- - REACT_113529
- - REACT_425969
- - REACT_428548
- - REACT_156540
- - REACT_1614597
- - REACT_351626
- - REACT_427899
- - seed.compound: cpd00067
- - unipathway.compound: UPC00080
- - !!omap
- - id: lac__D_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/h
+ - http://identifiers.org/biocyc/PROTON
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/cas/12408-02-5
+ - http://identifiers.org/chebi/CHEBI:24636
+ - http://identifiers.org/chebi/CHEBI:15378
+ - http://identifiers.org/chebi/CHEBI:10744
+ - http://identifiers.org/chebi/CHEBI:13357
+ - http://identifiers.org/chebi/CHEBI:5584
+ - http://identifiers.org/kegg.compound/C00080
+ - http://identifiers.org/pubchem.substance/3380
+ - http://identifiers.org/reactome/REACT_194688
+ - http://identifiers.org/reactome/REACT_425978
+ - http://identifiers.org/reactome/REACT_193465
+ - http://identifiers.org/reactome/REACT_374900
+ - http://identifiers.org/reactome/REACT_74722
+ - http://identifiers.org/reactome/REACT_425999
+ - http://identifiers.org/reactome/REACT_428040
+ - http://identifiers.org/reactome/REACT_163953
+ - http://identifiers.org/reactome/REACT_372511
+ - http://identifiers.org/reactome/REACT_2000349
+ - http://identifiers.org/reactome/REACT_70106
+ - http://identifiers.org/reactome/REACT_1470067
+ - http://identifiers.org/reactome/REACT_113529
+ - http://identifiers.org/reactome/REACT_425969
+ - http://identifiers.org/reactome/REACT_428548
+ - http://identifiers.org/reactome/REACT_156540
+ - http://identifiers.org/reactome/REACT_1614597
+ - http://identifiers.org/reactome/REACT_351626
+ - http://identifiers.org/reactome/REACT_427899
+ - http://identifiers.org/seed.compound/cpd00067
+ - http://identifiers.org/unipathway.compound/UPC00080
+ - !!omap
+ - id: M_lac__D_c
- name: D-Lactate
- compartment: c
- charge: -1
- formula: C3H5O3
- annotation: !!omap
- - bigg.metabolite: lac__D
- - biocyc: META:D-LACTATE
- - chebi:
- - CHEBI:11001
- - CHEBI:16004
- - CHEBI:18684
- - CHEBI:341
- - CHEBI:42105
- - CHEBI:42111
- - CHEBI:43701
- - hmdb:
- - HMDB00171
- - HMDB01311
- - kegg.compound: C00256
- - metanetx.chemical: MNXM285
- - seed.compound: cpd00221
- - !!omap
- - id: lac__D_e
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/lac__D
+ - http://identifiers.org/biocyc/META:D-LACTATE
+ - http://identifiers.org/chebi/CHEBI:11001
+ - http://identifiers.org/chebi/CHEBI:16004
+ - http://identifiers.org/chebi/CHEBI:18684
+ - http://identifiers.org/chebi/CHEBI:341
+ - http://identifiers.org/chebi/CHEBI:42105
+ - http://identifiers.org/chebi/CHEBI:42111
+ - http://identifiers.org/chebi/CHEBI:43701
+ - http://identifiers.org/hmdb/HMDB00171
+ - http://identifiers.org/hmdb/HMDB01311
+ - http://identifiers.org/kegg.compound/C00256
+ - http://identifiers.org/metanetx.chemical/MNXM285
+ - http://identifiers.org/seed.compound/cpd00221
+ - !!omap
+ - id: M_lac__D_e
- name: D-Lactate
- compartment: e
- charge: -1
- formula: C3H5O3
- annotation: !!omap
- - bigg.metabolite: lac__D
- - biocyc: META:D-LACTATE
- - chebi:
- - CHEBI:11001
- - CHEBI:16004
- - CHEBI:18684
- - CHEBI:341
- - CHEBI:42105
- - CHEBI:42111
- - CHEBI:43701
- - hmdb:
- - HMDB00171
- - HMDB01311
- - kegg.compound: C00256
- - metanetx.chemical: MNXM285
- - seed.compound: cpd00221
- - !!omap
- - id: nad_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/lac__D
+ - http://identifiers.org/biocyc/META:D-LACTATE
+ - http://identifiers.org/chebi/CHEBI:11001
+ - http://identifiers.org/chebi/CHEBI:16004
+ - http://identifiers.org/chebi/CHEBI:18684
+ - http://identifiers.org/chebi/CHEBI:341
+ - http://identifiers.org/chebi/CHEBI:42105
+ - http://identifiers.org/chebi/CHEBI:42111
+ - http://identifiers.org/chebi/CHEBI:43701
+ - http://identifiers.org/hmdb/HMDB00171
+ - http://identifiers.org/hmdb/HMDB01311
+ - http://identifiers.org/kegg.compound/C00256
+ - http://identifiers.org/metanetx.chemical/MNXM285
+ - http://identifiers.org/seed.compound/cpd00221
+ - !!omap
+ - id: M_nad_c
- name: Nicotinamide adenine dinucleotide
- compartment: c
- charge: -1
- formula: C21H26N7O14P2
- annotation: !!omap
- - bigg.metabolite: nad
- - biocyc: NAD
- - cas:
- - 53-84-9
- - chebi:
- - CHEBI:21901
- - CHEBI:7422
- - CHEBI:44214
- - CHEBI:15846
- - CHEBI:13394
- - CHEBI:13393
- - CHEBI:44215
- - CHEBI:13389
- - CHEBI:57540
- - CHEBI:44281
- - hmdb: HMDB00902
- - kegg.compound: C00003
- - kegg.drug: D00002
- - pubchem.substance: '3305'
- - reactome:
- - REACT_192307
- - REACT_29360
- - REACT_427523
- - REACT_194653
- - REACT_113526
- - seed.compound: cpd00003
- - unipathway.compound: UPC00003
- - !!omap
- - id: nadh_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/nad
+ - http://identifiers.org/biocyc/NAD
+ - http://identifiers.org/cas/53-84-9
+ - http://identifiers.org/cas/53-84-9
+ - http://identifiers.org/chebi/CHEBI:21901
+ - http://identifiers.org/chebi/CHEBI:7422
+ - http://identifiers.org/chebi/CHEBI:44214
+ - http://identifiers.org/chebi/CHEBI:15846
+ - http://identifiers.org/chebi/CHEBI:13394
+ - http://identifiers.org/chebi/CHEBI:13393
+ - http://identifiers.org/chebi/CHEBI:44215
+ - http://identifiers.org/chebi/CHEBI:13389
+ - http://identifiers.org/chebi/CHEBI:57540
+ - http://identifiers.org/chebi/CHEBI:44281
+ - http://identifiers.org/hmdb/HMDB00902
+ - http://identifiers.org/kegg.compound/C00003
+ - http://identifiers.org/kegg.drug/D00002
+ - http://identifiers.org/pubchem.substance/3305
+ - http://identifiers.org/reactome/REACT_192307
+ - http://identifiers.org/reactome/REACT_29360
+ - http://identifiers.org/reactome/REACT_427523
+ - http://identifiers.org/reactome/REACT_194653
+ - http://identifiers.org/reactome/REACT_113526
+ - http://identifiers.org/seed.compound/cpd00003
+ - http://identifiers.org/unipathway.compound/UPC00003
+ - !!omap
+ - id: M_nadh_c
- name: Nicotinamide adenine dinucleotide - reduced
- compartment: c
- charge: -2
- formula: C21H27N7O14P2
- annotation: !!omap
- - bigg.metabolite: nadh
- - biocyc: NADH
- - cas:
- - 58-68-4
- - chebi:
- - CHEBI:13395
- - CHEBI:21902
- - CHEBI:16908
- - CHEBI:7423
- - CHEBI:44216
- - CHEBI:57945
- - CHEBI:13396
- - hmdb: HMDB01487
- - kegg.compound: C00004
- - pubchem.substance: '3306'
- - reactome:
- - REACT_192305
- - REACT_73473
- - REACT_194697
- - REACT_29362
- - seed.compound: cpd00004
- - unipathway.compound: UPC00004
- - !!omap
- - id: pep_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/nadh
+ - http://identifiers.org/biocyc/NADH
+ - http://identifiers.org/cas/58-68-4
+ - http://identifiers.org/cas/58-68-4
+ - http://identifiers.org/chebi/CHEBI:13395
+ - http://identifiers.org/chebi/CHEBI:21902
+ - http://identifiers.org/chebi/CHEBI:16908
+ - http://identifiers.org/chebi/CHEBI:7423
+ - http://identifiers.org/chebi/CHEBI:44216
+ - http://identifiers.org/chebi/CHEBI:57945
+ - http://identifiers.org/chebi/CHEBI:13396
+ - http://identifiers.org/hmdb/HMDB01487
+ - http://identifiers.org/kegg.compound/C00004
+ - http://identifiers.org/pubchem.substance/3306
+ - http://identifiers.org/reactome/REACT_192305
+ - http://identifiers.org/reactome/REACT_73473
+ - http://identifiers.org/reactome/REACT_194697
+ - http://identifiers.org/reactome/REACT_29362
+ - http://identifiers.org/seed.compound/cpd00004
+ - http://identifiers.org/unipathway.compound/UPC00004
+ - !!omap
+ - id: M_pep_c
- name: Phosphoenolpyruvate
- compartment: c
- charge: -3
- formula: C3H2O6P
- annotation: !!omap
- - bigg.metabolite: pep
- - biocyc: PHOSPHO-ENOL-PYRUVATE
- - cas:
- - 138-08-9
- - chebi:
- - CHEBI:44897
- - CHEBI:44894
- - CHEBI:14812
- - CHEBI:8147
- - CHEBI:26055
- - CHEBI:26054
- - CHEBI:58702
- - CHEBI:18021
- - hmdb: HMDB00263
- - kegg.compound: C00074
- - pubchem.substance: '3374'
- - reactome:
- - REACT_29492
- - REACT_372364
- - seed.compound: cpd00061
- - unipathway.compound: UPC00074
- - !!omap
- - id: pi_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/pep
+ - http://identifiers.org/biocyc/PHOSPHO-ENOL-PYRUVATE
+ - http://identifiers.org/cas/138-08-9
+ - http://identifiers.org/cas/138-08-9
+ - http://identifiers.org/chebi/CHEBI:44897
+ - http://identifiers.org/chebi/CHEBI:44894
+ - http://identifiers.org/chebi/CHEBI:14812
+ - http://identifiers.org/chebi/CHEBI:8147
+ - http://identifiers.org/chebi/CHEBI:26055
+ - http://identifiers.org/chebi/CHEBI:26054
+ - http://identifiers.org/chebi/CHEBI:58702
+ - http://identifiers.org/chebi/CHEBI:18021
+ - http://identifiers.org/hmdb/HMDB00263
+ - http://identifiers.org/kegg.compound/C00074
+ - http://identifiers.org/pubchem.substance/3374
+ - http://identifiers.org/reactome/REACT_29492
+ - http://identifiers.org/reactome/REACT_372364
+ - http://identifiers.org/seed.compound/cpd00061
+ - http://identifiers.org/unipathway.compound/UPC00074
+ - !!omap
+ - id: M_pi_c
- name: Phosphate
- compartment: c
- charge: -2
- formula: HO4P
- annotation: !!omap
- - bigg.metabolite: pi
- - biocyc:
- - Pi
- - PHOSPHATE-GROUP
- - CPD0-1421
- - cas:
- - 14265-44-2
- - chebi:
- - CHEBI:37583
- - CHEBI:7793
- - CHEBI:37585
- - CHEBI:34683
- - CHEBI:14791
- - CHEBI:34855
- - CHEBI:29137
- - CHEBI:29139
- - CHEBI:63036
- - CHEBI:26020
- - CHEBI:39739
- - CHEBI:32597
- - CHEBI:32596
- - CHEBI:43474
- - CHEBI:63051
- - CHEBI:43470
- - CHEBI:9679
- - CHEBI:35433
- - CHEBI:4496
- - CHEBI:45024
- - CHEBI:18367
- - CHEBI:26078
- - CHEBI:39745
- - CHEBI:24838
- - hmdb: HMDB02142
- - kegg.compound:
- - C13556
- - C13558
- - C00009
- - kegg.drug: D05467
- - pubchem.substance: '3311'
- - reactome:
- - REACT_947590
- - REACT_109277
- - REACT_113548
- - REACT_2255331
- - REACT_29372
- - REACT_113550
- - REACT_113551
- - seed.compound:
- - cpd09464
- - cpd09463
- - cpd00009
- - unipathway.compound: UPC00009
- - !!omap
- - id: pi_e
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/pi
+ - http://identifiers.org/biocyc/Pi
+ - http://identifiers.org/biocyc/PHOSPHATE-GROUP
+ - http://identifiers.org/biocyc/CPD0-1421
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/chebi/CHEBI:37583
+ - http://identifiers.org/chebi/CHEBI:7793
+ - http://identifiers.org/chebi/CHEBI:37585
+ - http://identifiers.org/chebi/CHEBI:34683
+ - http://identifiers.org/chebi/CHEBI:14791
+ - http://identifiers.org/chebi/CHEBI:34855
+ - http://identifiers.org/chebi/CHEBI:29137
+ - http://identifiers.org/chebi/CHEBI:29139
+ - http://identifiers.org/chebi/CHEBI:63036
+ - http://identifiers.org/chebi/CHEBI:26020
+ - http://identifiers.org/chebi/CHEBI:39739
+ - http://identifiers.org/chebi/CHEBI:32597
+ - http://identifiers.org/chebi/CHEBI:32596
+ - http://identifiers.org/chebi/CHEBI:43474
+ - http://identifiers.org/chebi/CHEBI:63051
+ - http://identifiers.org/chebi/CHEBI:43470
+ - http://identifiers.org/chebi/CHEBI:9679
+ - http://identifiers.org/chebi/CHEBI:35433
+ - http://identifiers.org/chebi/CHEBI:4496
+ - http://identifiers.org/chebi/CHEBI:45024
+ - http://identifiers.org/chebi/CHEBI:18367
+ - http://identifiers.org/chebi/CHEBI:26078
+ - http://identifiers.org/chebi/CHEBI:39745
+ - http://identifiers.org/chebi/CHEBI:24838
+ - http://identifiers.org/hmdb/HMDB02142
+ - http://identifiers.org/kegg.compound/C13556
+ - http://identifiers.org/kegg.compound/C13558
+ - http://identifiers.org/kegg.compound/C00009
+ - http://identifiers.org/kegg.drug/D05467
+ - http://identifiers.org/pubchem.substance/3311
+ - http://identifiers.org/reactome/REACT_947590
+ - http://identifiers.org/reactome/REACT_109277
+ - http://identifiers.org/reactome/REACT_113548
+ - http://identifiers.org/reactome/REACT_2255331
+ - http://identifiers.org/reactome/REACT_29372
+ - http://identifiers.org/reactome/REACT_113550
+ - http://identifiers.org/reactome/REACT_113551
+ - http://identifiers.org/seed.compound/cpd09464
+ - http://identifiers.org/seed.compound/cpd09463
+ - http://identifiers.org/seed.compound/cpd00009
+ - http://identifiers.org/unipathway.compound/UPC00009
+ - !!omap
+ - id: M_pi_e
- name: Phosphate
- compartment: e
- charge: -2
- formula: HO4P
- annotation: !!omap
- - bigg.metabolite: pi
- - biocyc:
- - Pi
- - PHOSPHATE-GROUP
- - CPD0-1421
- - cas:
- - 14265-44-2
- - chebi:
- - CHEBI:37583
- - CHEBI:7793
- - CHEBI:37585
- - CHEBI:34683
- - CHEBI:14791
- - CHEBI:34855
- - CHEBI:29137
- - CHEBI:29139
- - CHEBI:63036
- - CHEBI:26020
- - CHEBI:39739
- - CHEBI:32597
- - CHEBI:32596
- - CHEBI:43474
- - CHEBI:63051
- - CHEBI:43470
- - CHEBI:9679
- - CHEBI:35433
- - CHEBI:4496
- - CHEBI:45024
- - CHEBI:18367
- - CHEBI:26078
- - CHEBI:39745
- - CHEBI:24838
- - hmdb: HMDB02142
- - kegg.compound:
- - C13556
- - C13558
- - C00009
- - kegg.drug: D05467
- - pubchem.substance: '3311'
- - reactome:
- - REACT_947590
- - REACT_109277
- - REACT_113548
- - REACT_2255331
- - REACT_29372
- - REACT_113550
- - REACT_113551
- - seed.compound:
- - cpd09464
- - cpd09463
- - cpd00009
- - unipathway.compound: UPC00009
- - !!omap
- - id: pyr_c
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/pi
+ - http://identifiers.org/biocyc/Pi
+ - http://identifiers.org/biocyc/PHOSPHATE-GROUP
+ - http://identifiers.org/biocyc/CPD0-1421
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/cas/14265-44-2
+ - http://identifiers.org/chebi/CHEBI:37583
+ - http://identifiers.org/chebi/CHEBI:7793
+ - http://identifiers.org/chebi/CHEBI:37585
+ - http://identifiers.org/chebi/CHEBI:34683
+ - http://identifiers.org/chebi/CHEBI:14791
+ - http://identifiers.org/chebi/CHEBI:34855
+ - http://identifiers.org/chebi/CHEBI:29137
+ - http://identifiers.org/chebi/CHEBI:29139
+ - http://identifiers.org/chebi/CHEBI:63036
+ - http://identifiers.org/chebi/CHEBI:26020
+ - http://identifiers.org/chebi/CHEBI:39739
+ - http://identifiers.org/chebi/CHEBI:32597
+ - http://identifiers.org/chebi/CHEBI:32596
+ - http://identifiers.org/chebi/CHEBI:43474
+ - http://identifiers.org/chebi/CHEBI:63051
+ - http://identifiers.org/chebi/CHEBI:43470
+ - http://identifiers.org/chebi/CHEBI:9679
+ - http://identifiers.org/chebi/CHEBI:35433
+ - http://identifiers.org/chebi/CHEBI:4496
+ - http://identifiers.org/chebi/CHEBI:45024
+ - http://identifiers.org/chebi/CHEBI:18367
+ - http://identifiers.org/chebi/CHEBI:26078
+ - http://identifiers.org/chebi/CHEBI:39745
+ - http://identifiers.org/chebi/CHEBI:24838
+ - http://identifiers.org/hmdb/HMDB02142
+ - http://identifiers.org/kegg.compound/C13556
+ - http://identifiers.org/kegg.compound/C13558
+ - http://identifiers.org/kegg.compound/C00009
+ - http://identifiers.org/kegg.drug/D05467
+ - http://identifiers.org/pubchem.substance/3311
+ - http://identifiers.org/reactome/REACT_947590
+ - http://identifiers.org/reactome/REACT_109277
+ - http://identifiers.org/reactome/REACT_113548
+ - http://identifiers.org/reactome/REACT_2255331
+ - http://identifiers.org/reactome/REACT_29372
+ - http://identifiers.org/reactome/REACT_113550
+ - http://identifiers.org/reactome/REACT_113551
+ - http://identifiers.org/seed.compound/cpd09464
+ - http://identifiers.org/seed.compound/cpd09463
+ - http://identifiers.org/seed.compound/cpd00009
+ - http://identifiers.org/unipathway.compound/UPC00009
+ - !!omap
+ - id: M_pyr_c
- name: Pyruvate
- compartment: c
- charge: -1
- formula: C3H3O3
- annotation: !!omap
- - bigg.metabolite: pyr
- - biocyc: PYRUVATE
- - cas:
- - 127-17-3
- - chebi:
- - CHEBI:15361
- - CHEBI:14987
- - CHEBI:8685
- - CHEBI:32816
- - CHEBI:45253
- - CHEBI:26466
- - CHEBI:26462
- - hmdb: HMDB00243
- - kegg.compound: C00022
- - lipidmaps: LMFA01060077
- - pubchem.substance: '3324'
- - reactome:
- - REACT_113557
- - REACT_389680
- - REACT_29398
- - seed.compound: cpd00020
- - unipathway.compound: UPC00022
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.metabolite/pyr
+ - http://identifiers.org/biocyc/PYRUVATE
+ - http://identifiers.org/cas/127-17-3
+ - http://identifiers.org/cas/127-17-3
+ - http://identifiers.org/chebi/CHEBI:15361
+ - http://identifiers.org/chebi/CHEBI:14987
+ - http://identifiers.org/chebi/CHEBI:8685
+ - http://identifiers.org/chebi/CHEBI:32816
+ - http://identifiers.org/chebi/CHEBI:45253
+ - http://identifiers.org/chebi/CHEBI:26466
+ - http://identifiers.org/chebi/CHEBI:26462
+ - http://identifiers.org/hmdb/HMDB00243
+ - http://identifiers.org/kegg.compound/C00022
+ - http://identifiers.org/lipidmaps/LMFA01060077
+ - http://identifiers.org/pubchem.substance/3324
+ - http://identifiers.org/reactome/REACT_113557
+ - http://identifiers.org/reactome/REACT_389680
+ - http://identifiers.org/reactome/REACT_29398
+ - http://identifiers.org/seed.compound/cpd00020
+ - http://identifiers.org/unipathway.compound/UPC00022
- reactions:
- !!omap
- - id: ATPM
+ - id: R_ATPM
- name: ATP maintenance requirement
- - metabolites: !!omap
- - adp_c: 1.0
- - atp_c: -1.0
- - h2o_c: -1.0
- - h_c: 1.0
- - pi_c: 1.0
- lower_bound: 8.39
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap
+ - M_atp_c: -1.0
+ - M_h2o_c: -1.0
+ - M_adp_c: 1.0
+ - M_h_c: 1.0
+ - M_pi_c: 1.0
- objective_coefficient: 1.0
- annotation: !!omap
- - bigg.reaction: ATPM
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/ATPM
- !!omap
- - id: D_LACt2
+ - id: R_D_LACt2
- name: ''
- - metabolites: !!omap []
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap []
- !!omap
- - id: ENO
+ - id: R_ENO
- name: enolase
- - metabolites: !!omap
- - 2pg_c: -1.0
- - h2o_c: 1.0
- - pep_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2779
+ - metabolites: !!omap
+ - M_2pg_c: -1.0
+ - M_pep_c: 1.0
+ - M_h2o_c: 1.0
- annotation: !!omap
- - bigg.reaction: ENO
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/ENO
- !!omap
- - id: EX_glc__D_e
+ - id: R_EX_glc__D_e
- name: D-Glucose exchange
- - metabolites: !!omap
- - glc__D_e: -1.0
- lower_bound: -10.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap
+ - M_glc__D_e: -1.0
- annotation: !!omap
- - bigg.reaction: glc
- sbo: SBO:0000627
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/glc
- !!omap
- - id: EX_h_e
+ - id: R_EX_h_e
- name: H+ exchange
- - metabolites: !!omap
- - h_e: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap
+ - M_h_e: -1.0
- annotation: !!omap
- - bigg.reaction: h
- sbo: SBO:0000627
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/h
- !!omap
- - id: EX_lac__D_e
+ - id: R_EX_lac__D_e
- name: D-lactate exchange
- - metabolites: !!omap
- - lac__D_e: -1.0
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: ''
+ - metabolites: !!omap
+ - M_lac__D_e: -1.0
- annotation: !!omap
- - bigg.reaction: lac__D
- sbo: SBO:0000627
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/lac__D
- !!omap
- - id: FBA
+ - id: R_FBA
- name: fructose-bisphosphate aldolase
- - metabolites: !!omap
- - dhap_c: 1.0
- - fdp_c: -1.0
- - g3p_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b1773 or b2097 or b2925
+ - metabolites: !!omap
+ - M_fdp_c: -1.0
+ - M_dhap_c: 1.0
+ - M_g3p_c: 1.0
- annotation: !!omap
- - bigg.reaction: FBA
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/FBA
- !!omap
- - id: GAPD
+ - id: R_GAPD
- name: glyceraldehyde-3-phosphate dehydrogenase
- - metabolites: !!omap
- - 13dpg_c: 1.0
- - g3p_c: -1.0
- - h_c: 1.0
- - nad_c: -1.0
- - nadh_c: 1.0
- - pi_c: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b1779
+ - metabolites: !!omap
+ - M_nad_c: -1.0
+ - M_13dpg_c: 1.0
+ - M_nadh_c: 1.0
+ - M_g3p_c: -1.0
+ - M_pi_c: -1.0
+ - M_h_c: 1.0
- annotation: !!omap
- - bigg.reaction: GAPD
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/GAPD
- !!omap
- - id: GLCpts
+ - id: R_GLCpts
- name: D-glucose transport via PEP:Pyr PTS
- - metabolites: !!omap
- - g6p_c: 1.0
- - glc__D_e: -1.0
- - pep_c: -1.0
- - pyr_c: 1.0
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: (b2415 and b2417 and b1101 and b2416) or (b2415 and b2417
and b1621 and b2416) or (b2415 and b1818 and b1817 and b1819 and b2416)
+ - metabolites: !!omap
+ - M_g6p_c: 1.0
+ - M_pyr_c: 1.0
+ - M_glc__D_e: -1.0
+ - M_pep_c: -1.0
- annotation: !!omap
- - bigg.reaction: GLCpts
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/GLCpts
- !!omap
- - id: H2Ot
+ - id: R_H2Ot
- name: R H2O transport via - diffusion
- - metabolites: !!omap
- - h2o_c: 1.0
- - h2o_e: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b0875 or s0001
+ - metabolites: !!omap
+ - M_h2o_e: -1.0
+ - M_h2o_c: 1.0
- annotation: !!omap
- - bigg.reaction: H2Ot
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/H2Ot
- !!omap
- - id: LDH_D
+ - id: R_LDH_D
- name: D-lactate dehydrogenase
- - metabolites: !!omap
- - h_c: 1.0
- - lac__D_c: -1.0
- - nad_c: -1.0
- - nadh_c: 1.0
- - pyr_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2133 or b1380
+ - metabolites: !!omap
+ - M_lac__D_c: -1.0
+ - M_nad_c: -1.0
+ - M_h_c: 1.0
+ - M_nadh_c: 1.0
+ - M_pyr_c: 1.0
- subsystem: Pyruvate Metabolism
- annotation: !!omap
- - bigg.reaction: LDH_D
- - biocyc: META:DLACTDEHYDROGNAD-RXN
- - ec-code: 1.1.1.28
- - kegg.reaction: R00704
- - metanetx.reaction: MNXR101037
- - rhea:
- - '16369'
- - '16370'
- - '16371'
- - '16372'
- sbo: SBO:0000375
- - !!omap
- - id: PFK
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/LDH_D
+ - http://identifiers.org/biocyc/META:DLACTDEHYDROGNAD-RXN
+ - http://identifiers.org/ec-code/1.1.1.28
+ - http://identifiers.org/kegg.reaction/R00704
+ - http://identifiers.org/metanetx.reaction/MNXR101037
+ - http://identifiers.org/rhea/16369
+ - http://identifiers.org/rhea/16370
+ - http://identifiers.org/rhea/16371
+ - http://identifiers.org/rhea/16372
+ - !!omap
+ - id: R_PFK
- name: phosphofructokinase
- - metabolites: !!omap
- - adp_c: 1.0
- - atp_c: -1.0
- - f6p_c: -1.0
- - fdp_c: 1.0
- - h_c: 1.0
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: b3916 or b1723
+ - metabolites: !!omap
+ - M_f6p_c: -1.0
+ - M_atp_c: -1.0
+ - M_adp_c: 1.0
+ - M_fdp_c: 1.0
+ - M_h_c: 1.0
- objective_coefficient: 1.0
- annotation: !!omap
- - bigg.reaction: PFK
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/PFK
- !!omap
- - id: PGI
+ - id: R_PGI
- name: glucose-6-phosphate isomerase
- - metabolites: !!omap
- - f6p_c: 1.0
- - g6p_c: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b4025
+ - metabolites: !!omap
+ - M_g6p_c: -1.0
+ - M_f6p_c: 1.0
- annotation: !!omap
- - bigg.reaction: PGI
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/PGI
- !!omap
- - id: PGK
+ - id: R_PGK
- name: phosphoglycerate kinase
- - metabolites: !!omap
- - 13dpg_c: 1.0
- - 3pg_c: -1.0
- - adp_c: 1.0
- - atp_c: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2926
+ - metabolites: !!omap
+ - M_3pg_c: -1.0
+ - M_atp_c: -1.0
+ - M_13dpg_c: 1.0
+ - M_adp_c: 1.0
- annotation: !!omap
- - bigg.reaction: PGK
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/PGK
- !!omap
- - id: PGM
+ - id: R_PGM
- name: phosphoglycerate mutase
- - metabolites: !!omap
- - 2pg_c: -1.0
- - 3pg_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b4395 or b3612 or b0755
+ - metabolites: !!omap
+ - M_2pg_c: -1.0
+ - M_3pg_c: 1.0
- annotation: !!omap
- - bigg.reaction: PGM
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/PGM
- !!omap
- - id: PIt2r
+ - id: R_PIt2r
- name: R phosphate reversible transport via - symport
- - metabolites: !!omap
- - h_c: 1.0
- - h_e: -1.0
- - pi_c: 1.0
- - pi_e: -1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b2987 or b3493
+ - metabolites: !!omap
+ - M_pi_e: -1.0
+ - M_h_e: -1.0
+ - M_h_c: 1.0
+ - M_pi_c: 1.0
- annotation: !!omap
- - bigg.reaction: PIt2r
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/PIt2r
- !!omap
- - id: PYK
+ - id: R_PYK
- name: pyruvate kinase
- - metabolites: !!omap
- - adp_c: -1.0
- - atp_c: 1.0
- - h_c: -1.0
- - pep_c: -1.0
- - pyr_c: 1.0
- lower_bound: 0.0
- upper_bound: 1000.0
- gene_reaction_rule: b1854 or b1676
+ - metabolites: !!omap
+ - M_adp_c: -1.0
+ - M_h_c: -1.0
+ - M_pep_c: -1.0
+ - M_atp_c: 1.0
+ - M_pyr_c: 1.0
- annotation: !!omap
- - bigg.reaction: PYK
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/PYK
- !!omap
- - id: TPI
+ - id: R_TPI
- name: triose-phosphate isomerase
- - metabolites: !!omap
- - dhap_c: -1.0
- - g3p_c: 1.0
- lower_bound: -1000.0
- upper_bound: 1000.0
- gene_reaction_rule: b3919
+ - metabolites: !!omap
+ - M_dhap_c: -1.0
+ - M_g3p_c: 1.0
- annotation: !!omap
- - bigg.reaction: TPI
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/bigg.reaction/TPI
- genes:
- !!omap
- - id: b0755
+ - id: G_b0755
- name: gpmA
- !!omap
- - id: b0875
+ - id: G_b0875
- name: aqpZ
- !!omap
- - id: b1101
+ - id: G_b1101
- name: ptsG
- !!omap
- - id: b1380
+ - id: G_b1380
- name: ldhA
- !!omap
- - id: b1621
+ - id: G_b1621
- name: malX
- !!omap
- - id: b1676
+ - id: G_b1676
- name: pykF
- annotation: !!omap
- - ncbiprotein:
- - '1208453'
- - '1652654'
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/ncbiprotein/1208453
+ - http://identifiers.org/ncbiprotein/1652654
- !!omap
- - id: b1723
+ - id: G_b1723
- name: pfkB
- !!omap
- - id: b1773
+ - id: G_b1773
- name: ydjI
- !!omap
- - id: b1779
+ - id: G_b1779
- name: gapA
- !!omap
- - id: b1817
+ - id: G_b1817
- name: manX
- !!omap
- - id: b1818
+ - id: G_b1818
- name: manY
- !!omap
- - id: b1819
+ - id: G_b1819
- name: manZ
- !!omap
- - id: b1854
+ - id: G_b1854
- name: pykA
- !!omap
- - id: b2097
+ - id: G_b2097
- name: fbaB
- !!omap
- - id: b2133
+ - id: G_b2133
- name: dld
- !!omap
- - id: b2415
+ - id: G_b2415
- name: ptsH
- !!omap
- - id: b2416
+ - id: G_b2416
- name: ptsI
- !!omap
- - id: b2417
+ - id: G_b2417
- name: crr
- !!omap
- - id: b2779
+ - id: G_b2779
- name: eno
- annotation: !!omap
- - ncbiprotein: '1653839'
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/ncbiprotein/1653839
- !!omap
- - id: b2925
+ - id: G_b2925
- name: fbaA
- !!omap
- - id: b2926
+ - id: G_b2926
- name: pgk
- annotation: !!omap
- - ncbiprotein: '1653609'
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/ncbiprotein/1653609
- !!omap
- - id: b2987
+ - id: G_b2987
- name: pitB
- !!omap
- - id: b3493
+ - id: G_b3493
- name: pitA
- !!omap
- - id: b3612
+ - id: G_b3612
- name: gpmM
- !!omap
- - id: b3916
+ - id: G_b3916
- name: pfkA
- annotation: !!omap
- - ncbiprotein:
- - '1006614'
- - '1651919'
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/ncbiprotein/1006614
+ - http://identifiers.org/ncbiprotein/1651919
- !!omap
- - id: b3919
+ - id: G_b3919
- name: tpiA
- !!omap
- - id: b4025
+ - id: G_b4025
- name: pgi
- annotation: !!omap
- - ncbiprotein: '1653253'
+ - standardized: !!omap
+ - bqb_is:
+ - resources:
+ - http://identifiers.org/ncbiprotein/1653253
- !!omap
- - id: b4395
+ - id: G_b4395
- name: ytjC
- !!omap
- - id: s0001
+ - id: G_s0001
- name: G_s0001
+- groups: []
- id: mini_textbook
- compartments: !!omap
- c: cytosol
diff --git a/src/cobra/data/mini_cobra.xml b/src/cobra/data/mini_cobra.xml
index bc0d31f38..a22f61a4a 100644
--- a/src/cobra/data/mini_cobra.xml
+++ b/src/cobra/data/mini_cobra.xml
@@ -21,19 +21,19 @@
-
-
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+
+
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+
@@ -46,23 +46,23 @@
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@@ -75,29 +75,29 @@
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@@ -149,32 +150,33 @@
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diff --git a/src/cobra/flux_analysis/reaction.py b/src/cobra/flux_analysis/reaction.py
index d3f146d4a..ebc8a1e9a 100644
--- a/src/cobra/flux_analysis/reaction.py
+++ b/src/cobra/flux_analysis/reaction.py
@@ -58,13 +58,14 @@ def assess(
if m.slim_optimize(error_value=0.0) >= flux_coefficient_cutoff:
return True
else:
- results = {}
- results["precursors"] = assess_component(
- model, reaction, "reactants", flux_coefficient_cutoff
- )
- results["products"] = assess_component(
- model, reaction, "products", flux_coefficient_cutoff
- )
+ results = {
+ "precursors": assess_component(
+ model, reaction, "reactants", flux_coefficient_cutoff
+ ),
+ "products": assess_component(
+ model, reaction, "products", flux_coefficient_cutoff
+ ),
+ }
return results
diff --git a/src/cobra/io/__init__.py b/src/cobra/io/__init__.py
index 66d8a1b92..4c7ac6135 100644
--- a/src/cobra/io/__init__.py
+++ b/src/cobra/io/__init__.py
@@ -2,8 +2,14 @@
from cobra.io.dict import model_from_dict, model_to_dict
-from cobra.io.json import from_json, load_json_model, save_json_model, to_json
-from cobra.io.mat import load_matlab_model, save_matlab_model
+from cobra.io.json import (
+ from_json,
+ load_json_model,
+ save_json_model,
+ to_json,
+ validate_json_model,
+)
+from cobra.io.mat import load_matlab_model, save_matlab_model, create_mat_dict
from cobra.io.sbml import read_sbml_model, write_sbml_model, validate_sbml_model
from cobra.io.yaml import from_yaml, load_yaml_model, save_yaml_model, to_yaml
from cobra.io.web import AbstractModelRepository, BiGGModels, BioModels, load_model
diff --git a/src/cobra/io/dict.py b/src/cobra/io/dict.py
index b0f009d4c..73f565dc9 100644
--- a/src/cobra/io/dict.py
+++ b/src/cobra/io/dict.py
@@ -1,12 +1,25 @@
"""Provide functions for cobrapy objects to generic Python objects and vice-versa."""
-
-from collections import OrderedDict
-from operator import attrgetter, itemgetter
-from typing import TYPE_CHECKING, Dict, List, Sequence, Set, Union
+import itertools
+import re
+from collections import OrderedDict, defaultdict
+from typing import TYPE_CHECKING, Dict, List, Sequence, Set, Tuple, Union
import numpy as np
-from ..core import Gene, Metabolite, Model, Reaction
+from ..core import Gene, Group, Metabolite, Model, Reaction
+from ..core.metadata import MetaData
+from ..core.metadata.helper import URL_IDENTIFIERS_PATTERN, parse_identifiers_uri
+from ..io.sbml import (
+ F_GENE,
+ F_GENE_REV,
+ F_GROUP,
+ F_GROUP_REV,
+ F_REACTION,
+ F_REACTION_REV,
+ F_REPLACE,
+ F_SPECIE,
+ F_SPECIE_REV,
+)
from ..util.solver import set_objective
@@ -16,7 +29,6 @@
_REQUIRED_REACTION_ATTRIBUTES = [
"id",
"name",
- "metabolites",
"lower_bound",
"upper_bound",
"gene_reaction_rule",
@@ -57,6 +69,14 @@
"annotation": {},
}
+_REQUIRED_GROUP_ATTRIBUTES = ["id", "kind", "members"]
+_ORDERED_OPTIONAL_GROUP_KEYS = ["name", "notes", "annotation"]
+_OPTIONAL_GROUP_ATTRIBUTES = {
+ "name": "",
+ "notes": {},
+ "annotation": {},
+}
+
_ORDERED_OPTIONAL_MODEL_KEYS = ["name", "compartments", "notes", "annotation"]
_OPTIONAL_MODEL_ATTRIBUTES = {
"name": None,
@@ -67,9 +87,25 @@
}
+def flatten(list_of_lists: Union[List, Tuple]) -> List:
+ """Flatten lists of lists.
+
+ Parameters
+ ----------
+ list_of_lists: List or Tuple
+ List or Tuple of lists or tuples to flatten.
+
+ Returns
+ -------
+ list: flattened list
+
+ """
+ return list(itertools.chain.from_iterable(list_of_lists))
+
+
def _fix_type(
value: Union[str, np.float, np.bool, Set, Dict]
-) -> Union[str, float, bool, List, OrderedDict]:
+) -> Union[str, float, bool, List, OrderedDict, Dict]:
"""Convert possible types to correct Python types.
Parameters
@@ -86,6 +122,8 @@ def _fix_type(
# Because numpy floats can not be pickled to json
if isinstance(value, str):
return str(value)
+ if isinstance(value, np.float) and (np.isnan(value) or np.isinf(value)):
+ return str(value)
if isinstance(value, np.float):
return float(value)
if isinstance(value, np.bool):
@@ -94,6 +132,8 @@ def _fix_type(
return list(value)
if isinstance(value, dict):
return OrderedDict((key, value[key]) for key in sorted(value))
+ if isinstance(value, MetaData):
+ return value.to_dict()
# handle legacy Formula type
if value.__class__.__name__ == "Formula":
return str(value)
@@ -131,19 +171,78 @@ def _update_optional(
"""
for key in ordered_keys:
default = optional_attribute_dict[key]
- value = getattr(cobra_object, key)
+ value = getattr(cobra_object, key, None)
if value is None or value == default:
continue
new_dict[key] = _fix_type(value)
-def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict:
+def _fix_id_from_dict(
+ _id_to_fix: str,
+ _class_to_fix_to: str,
+ f_replace: dict = F_REPLACE, # noqa: W0102
+):
+ if f_replace is None:
+ f_replace = {}
+ if not f_replace:
+ return _id_to_fix
+ if _class_to_fix_to == "Metabolite":
+ return F_REPLACE[F_SPECIE](_id_to_fix)
+ elif _class_to_fix_to == "Reaction":
+ return F_REPLACE[F_REACTION](_id_to_fix)
+ elif _class_to_fix_to == "Gene":
+ return F_REPLACE[F_GENE](_id_to_fix)
+ elif _class_to_fix_to == "Group":
+ return F_REPLACE[F_GROUP](_id_to_fix)
+
+
+def _fix_value_from_dict(_key: str, _value_to_fix: Union[List, str]):
+ if _key == "annotation":
+ # if annotation is in the form of list of list, modify the format
+ # https://github.com/opencobra/cobrapy/issues/736
+ if isinstance(_value_to_fix, list) and isinstance(_value_to_fix[0], list):
+ _value_to_fix = flatten(_value_to_fix)
+ anno_dict = defaultdict(list)
+ if isinstance(_value_to_fix, list):
+ for item in _value_to_fix:
+ if re.match(URL_IDENTIFIERS_PATTERN, item):
+ provider, identifier = parse_identifiers_uri(item)
+ anno_dict[provider].append(identifier)
+ _value_to_fix = anno_dict
+ _value_to_fix = MetaData.from_dict(_value_to_fix)
+ elif _key == "lower_bound" or _key == "upper_bound":
+ _value_to_fix = float(_value_to_fix)
+
+ return _value_to_fix
+
+
+def _get_by_id(
+ _id: str, _object_to_get: str, model: Model
+) -> Union[Gene, Metabolite, Group, Reaction]:
+ if _object_to_get == "Reaction":
+ return model.reactions.get_by_id(_id)
+ elif _object_to_get == "Metabolite":
+ return model.metabolites.get_by_id(_id)
+ elif _object_to_get == "Group":
+ return model.groups.get_by_id(_id)
+ elif _object_to_get == "Gene":
+ return model.genes.get_by_id(_id)
+
+
+def _metabolite_to_dict(
+ metabolite: Metabolite, f_replace: dict = F_REPLACE # noqa: W0102
+) -> OrderedDict:
"""Convert a cobra Metabolite object to dictionary.
Parameters
----------
metabolite : cobra.Metabolite
The cobra.Metabolite to convert to dictionary.
+ f_replace : dict of replacement functions for id replacement
+ Dictionary of replacement functions for gene, specie, and reaction.
+ By default, the following id changes are performed on import:
+ clip G_ from genes, clip M_ from species, clip R_ from reactions
+ If no replacements should be performed, set f_replace={} or None
Returns
-------
@@ -155,9 +254,15 @@ def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict:
_metabolite_from_dict : Convert a dictionary to cobra Metabolite object.
"""
+ if f_replace is None:
+ f_replace = {}
+
new_metabolite = OrderedDict()
for key in _REQUIRED_METABOLITE_ATTRIBUTES:
- new_metabolite[key] = _fix_type(getattr(metabolite, key))
+ if key == "id" and f_replace and F_SPECIE_REV in f_replace:
+ new_metabolite[key] = _fix_type(f_replace[F_SPECIE_REV](metabolite.id))
+ else:
+ new_metabolite[key] = _fix_type(getattr(metabolite, key))
_update_optional(
metabolite,
new_metabolite,
@@ -167,7 +272,9 @@ def _metabolite_to_dict(metabolite: Metabolite) -> OrderedDict:
return new_metabolite
-def _metabolite_from_dict(metabolite: Dict) -> Metabolite:
+def _metabolite_from_dict(
+ metabolite: Dict, f_replace: dict = F_REPLACE # noqa: W0102
+) -> Metabolite:
"""Convert a dictionary to cobra Metabolite object.
Parameters
@@ -184,9 +291,17 @@ def _metabolite_from_dict(metabolite: Dict) -> Metabolite:
_metabolite_to_dict : Convert a cobra Metabolite object to dictionary.
"""
- new_metabolite = Metabolite()
- for k, v in metabolite.items():
- setattr(new_metabolite, k, v)
+ if f_replace is None:
+ f_replace = {}
+
+ new_metabolite = Metabolite(
+ _fix_id_from_dict(metabolite["id"], "Metabolite", f_replace)
+ )
+ [
+ setattr(new_metabolite, k, _fix_value_from_dict(k, v))
+ for k, v in metabolite.items()
+ if k != "id"
+ ]
return new_metabolite
@@ -210,14 +325,17 @@ def _gene_to_dict(gene: Gene) -> OrderedDict:
"""
new_gene = OrderedDict()
for key in _REQUIRED_GENE_ATTRIBUTES:
- new_gene[key] = _fix_type(getattr(gene, key))
+ if key == "id":
+ new_gene[key] = _fix_type(F_REPLACE["F_GENE_REV"](gene.id))
+ else:
+ new_gene[key] = _fix_type(getattr(gene, key))
_update_optional(
gene, new_gene, _OPTIONAL_GENE_ATTRIBUTES, _ORDERED_OPTIONAL_GENE_KEYS
)
return new_gene
-def gene_from_dict(gene: Dict) -> Gene:
+def gene_from_dict(gene: Dict, f_replace: dict = F_REPLACE) -> Gene: # noqa: W0102
"""Convert a dictionary to cobra Gene object.
Parameters
@@ -235,9 +353,15 @@ def gene_from_dict(gene: Dict) -> Gene:
_gene_to_dict : Convert a cobra Gene object to a dictionary.
"""
- new_gene = Gene(gene["id"])
- for k, v in gene.items():
- setattr(new_gene, k, v)
+ if f_replace is None:
+ f_replace = {}
+
+ new_gene = Gene(_fix_id_from_dict(gene["id"], "Gene", f_replace))
+ [
+ setattr(new_gene, k, _fix_value_from_dict(k, v))
+ for k, v in gene.items()
+ if k != "id"
+ ]
return new_gene
@@ -261,22 +385,18 @@ def _reaction_to_dict(reaction: Reaction) -> OrderedDict:
"""
new_reaction = OrderedDict()
for key in _REQUIRED_REACTION_ATTRIBUTES:
- if key != "metabolites":
- if key == "lower_bound" and (
- np.isnan(reaction.lower_bound) or np.isinf(reaction.lower_bound)
- ):
- new_reaction[key] = str(_fix_type(getattr(reaction, key)))
- elif key == "upper_bound" and (
- np.isnan(reaction.upper_bound) or np.isinf(reaction.upper_bound)
- ):
- new_reaction[key] = str(_fix_type(getattr(reaction, key)))
- else:
- new_reaction[key] = _fix_type(getattr(reaction, key))
- continue
- mets = OrderedDict()
- for met in sorted(reaction.metabolites, key=attrgetter("id")):
- mets[str(met)] = reaction.metabolites[met]
- new_reaction["metabolites"] = mets
+ if key == "id":
+ new_reaction[key] = _fix_type(F_REPLACE[F_REACTION_REV](reaction.id))
+ else:
+ new_reaction[key] = _fix_type(getattr(reaction, key))
+ if F_REPLACE and F_SPECIE_REV in F_REPLACE:
+ mets = {
+ F_REPLACE[F_SPECIE_REV](met.id): stoic
+ for met, stoic in reaction.metabolites.items()
+ }
+ else:
+ mets = {met.id: stoic for met, stoic in reaction.metabolites.items()}
+ new_reaction["metabolites"] = OrderedDict(mets)
_update_optional(
reaction,
new_reaction,
@@ -286,7 +406,9 @@ def _reaction_to_dict(reaction: Reaction) -> OrderedDict:
return new_reaction
-def _reaction_from_dict(reaction: Dict, model: Model) -> Reaction:
+def _reaction_from_dict(
+ reaction: Dict, model: Model, f_replace: Dict = F_REPLACE # noqa: W0102
+) -> Reaction:
"""Convert a dictionary to a cobra Reaction object.
Parameters
@@ -306,26 +428,93 @@ def _reaction_from_dict(reaction: Dict, model: Model) -> Reaction:
_reaction_to_dict : Convert a cobra Reaction object to a dictionary.
"""
- new_reaction = Reaction()
- for k, v in reaction.items():
- if k in {"objective_coefficient", "reversibility", "reaction"}:
- continue
- elif k == "metabolites":
- new_reaction.add_metabolites(
- OrderedDict(
- (model.metabolites.get_by_id(str(met)), coeff)
- for met, coeff in v.items()
- )
+ if f_replace is None:
+ f_replace = {}
+
+ new_reaction = Reaction(_fix_id_from_dict(reaction["id"], "Reaction", f_replace))
+ [
+ setattr(new_reaction, k, _fix_value_from_dict(k, v))
+ for k, v in reaction.items()
+ if k
+ not in {
+ "id",
+ "objective_coefficient",
+ "reversibility",
+ "reaction",
+ "metabolites",
+ }
+ ]
+
+ new_reaction.add_metabolites(
+ OrderedDict(
+ (
+ model.metabolites.get_by_id(
+ _fix_id_from_dict(str(met), "Metabolite", f_replace)
+ ),
+ coeff,
)
- else:
- if k == "lower_bound" or k == "upper_bound":
- setattr(new_reaction, k, float(v))
- else:
- setattr(new_reaction, k, v)
+ for met, coeff in reaction.get("metabolites", {}).items()
+ )
+ )
return new_reaction
-def model_to_dict(model: Model, sort: bool = False) -> OrderedDict:
+def group_to_dict(group: "Group") -> Dict:
+ new_group = OrderedDict()
+ for key in _REQUIRED_GROUP_ATTRIBUTES:
+ if key != "members":
+ if key == "id":
+ new_group[key] = _fix_type(F_REPLACE[F_GROUP_REV](group.id))
+ else:
+ new_group[key] = _fix_type(getattr(group, key))
+ continue
+ members = []
+ for member in group.members:
+ idRef = member.id
+ if isinstance(member, Reaction):
+ idRef = F_REPLACE[F_REACTION_REV](member.id)
+ elif isinstance(member, Gene):
+ idRef = F_REPLACE[F_GENE_REV](member.id)
+ elif isinstance(member, Metabolite):
+ idRef = F_REPLACE[F_SPECIE_REV](member.id)
+ elif isinstance(member, Group):
+ idRef = F_REPLACE[F_GROUP_REV](member.id)
+ json_member = {"idRef": idRef, "type": type(member).__name__}
+ members.append(json_member)
+ new_group["members"] = members
+ _update_optional(
+ group, new_group, _OPTIONAL_GROUP_ATTRIBUTES, _ORDERED_OPTIONAL_GROUP_KEYS
+ )
+ return new_group
+
+
+def group_from_dict(
+ group: Dict, model: Model, f_replace=F_REPLACE # noqa: W0102
+) -> Group:
+ if f_replace is None:
+ f_replace = {}
+
+ new_group = Group(_fix_id_from_dict(group["id"], "Group"))
+ [
+ setattr(new_group, k, _fix_value_from_dict(k, v))
+ for k, v in group.items()
+ if k not in {"id", "members"}
+ ]
+ cobra_members = [
+ _get_by_id(
+ _fix_id_from_dict(member["idRef"], member["type"], f_replace),
+ member["type"],
+ model,
+ )
+ for member in group["members"]
+ ]
+ new_group.add_members(cobra_members)
+ return new_group
+
+
+def model_to_dict(
+ model: Model, sort: bool = False, f_replace: dict = F_REPLACE # noqa: W0102
+) -> OrderedDict:
"""Convert a cobra Model to a dictionary.
Parameters
@@ -335,6 +524,11 @@ def model_to_dict(model: Model, sort: bool = False) -> OrderedDict:
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model (default False).
+ f_replace : dict of replacement functions for id replacement
+ Dictionary of replacement functions for gene, specie, and reaction.
+ By default, the following id changes are performed on import:
+ clip G_ from genes, clip M_ from species, clip R_ from reactions
+ If no replacements should be performed, set f_replace={} or None
Returns
-------
@@ -349,19 +543,29 @@ def model_to_dict(model: Model, sort: bool = False) -> OrderedDict:
model_from_dict : Convert a dictionary to a cobra Model.
"""
+ if f_replace is None:
+ f_replace = {}
+
obj = OrderedDict()
obj["metabolites"] = list(map(_metabolite_to_dict, model.metabolites))
obj["reactions"] = list(map(_reaction_to_dict, model.reactions))
obj["genes"] = list(map(_gene_to_dict, model.genes))
+ obj["groups"] = list(map(group_to_dict, model.groups))
+
+ # sbml meta info
+ if hasattr(model, "_sbml"):
+ obj["sbml_info"] = OrderedDict(
+ {key: _fix_type(value) for key, value in model._sbml.items()}
+ )
obj["id"] = model.id
_update_optional(
model, obj, _OPTIONAL_MODEL_ATTRIBUTES, _ORDERED_OPTIONAL_MODEL_KEYS
)
if sort:
- get_id = itemgetter("id")
- obj["metabolites"].sort(key=get_id)
- obj["reactions"].sort(key=get_id)
- obj["genes"].sort(key=get_id)
+ obj["metabolites"].sort(key=lambda x: x["id"])
+ obj["reactions"].sort(key=lambda x: x["id"])
+ obj["genes"].sort(key=lambda x: x["id"])
+ obj["groups"].sort(key=lambda x: x["id"])
return obj
@@ -408,11 +612,24 @@ def model_from_dict(obj: Dict) -> Model:
rxn for rxn in obj["reactions"] if rxn.get("objective_coefficient", 0) != 0
]
coefficients = {
- model.reactions.get_by_id(rxn["id"]): rxn["objective_coefficient"]
+ model.reactions.get_by_id(F_REPLACE["F_REACTION"](rxn["id"])): rxn[
+ "objective_coefficient"
+ ]
for rxn in objective_reactions
}
+ if "groups" in obj:
+ model.add_groups([group_from_dict(group, model) for group in obj["groups"]])
set_objective(model, coefficients)
- for k, v in obj.items():
- if k in {"id", "name", "notes", "compartments", "annotation"}:
- setattr(model, k, v)
+
+ # sbml meta info
+ if "sbml_info" in obj:
+ meta = {k: _fix_value_from_dict(k, v) for k, v in obj["sbml_info"].items()}
+ model._sbml = meta
+
+ [
+ setattr(model, k, _fix_value_from_dict(k, v))
+ for k, v in obj.items()
+ if k in {"id", "name", "compartments", "annotation", "notes"}
+ ]
+
return model
diff --git a/src/cobra/io/json.py b/src/cobra/io/json.py
index 8fec5191d..31c20be70 100644
--- a/src/cobra/io/json.py
+++ b/src/cobra/io/json.py
@@ -1,6 +1,11 @@
"""Provide functions for I/O in JSON format."""
from pathlib import Path
-from typing import TYPE_CHECKING, Any, Union
+from typing import TYPE_CHECKING, Any, Dict, List, Union
+
+import jsonschema
+from importlib_resources import files
+
+from cobra import io as cio
from .dict import model_from_dict, model_to_dict
@@ -17,6 +22,18 @@
JSON_SPEC = "1"
+def json_schema_v1() -> Dict:
+ with files(cio).joinpath("schema_v1.json").open("r") as handle:
+ schema_v1 = json.load(handle)
+ return schema_v1
+
+
+def json_schema_v2() -> Dict:
+ with files(cio).joinpath("schema_v2.json").open("r") as handle:
+ schema_v2 = json.load(handle)
+ return schema_v2
+
+
def to_json(model: "Model", sort: bool = False, **kwargs: Any) -> str:
"""Return the model as a JSON string.
@@ -72,7 +89,7 @@ def save_json_model(
filename: Union[str, Path],
sort: bool = False,
pretty: bool = False,
- **kwargs: Any
+ **kwargs: Any,
) -> None:
"""Write the cobra model to a file in JSON format.
@@ -80,7 +97,7 @@ def save_json_model(
----------
model : cobra.Model
The cobra model to represent.
- filename : str or file-like
+ filename : str or file-like or Path
File path or descriptor that the JSON representation should be
written to.
sort : bool, optional
@@ -130,7 +147,7 @@ def load_json_model(filename: Union[str, Path]) -> "Model":
Parameters
----------
- filename : str or file-like
+ filename : str or file-like or Path
File path or descriptor that contains the JSON document describing the
cobra model.
@@ -149,3 +166,48 @@ def load_json_model(filename: Union[str, Path]) -> "Model":
return model_from_dict(json.load(file_handle))
else:
return model_from_dict(json.load(filename))
+
+
+def validate_json_model(
+ filename: Union[str, bytes], json_schema_version: int = 1
+) -> List:
+ """
+ Validate a model in json format against the schema with given version
+ Parameters
+ ----------
+ filename : str or file-like
+ File path or descriptor that contains the JSON document describing the
+ cobra model.
+ json_schema_version : int {1, 2}
+ the version of schema to be used for validation.
+ Currently we have v1 and v2 only and v2 is under development
+ Returns
+ -------
+ errors : list
+ The list of errors encountered while validating
+ """
+
+ if json_schema_version == 1:
+ schema = json_schema_v1()
+ elif json_schema_version == 2:
+ schema = json_schema_v2()
+ else:
+ raise ValueError(
+ f"Only v1 and v2 of JSON schema are available. JSON "
+ f"schema v{json_schema_version} is not supported."
+ )
+
+ # TODO - Should the validator be picked by schema?
+ # Something like validators.validator_for
+ validator = jsonschema.Draft7Validator(schema)
+
+ try:
+ if isinstance(filename, (str, Path)):
+ with open(filename, "r") as file_handle:
+ errors = validator.iter_errors(json.load(file_handle))
+ else:
+ errors = validator.iter_errors(json.load(filename))
+ except OSError:
+ errors = validator.iter_errors(json.loads(filename))
+
+ return list(errors)
diff --git a/src/cobra/io/mat.py b/src/cobra/io/mat.py
index ae436b646..6efe0d48b 100644
--- a/src/cobra/io/mat.py
+++ b/src/cobra/io/mat.py
@@ -908,7 +908,7 @@ def from_mat_struct(
new_group = Group(
id=g_name, name=g_name, members=group_members, kind="partonomy"
)
- new_group.annotation["sbo"] = "SBO:0000633"
+ new_group.annotation["sbo"] = ["SBO:0000633"]
new_groups.append(new_group)
model.add_groups(new_groups)
diff --git a/src/cobra/io/sbml.py b/src/cobra/io/sbml.py
index 48eed544b..2f2cfd96b 100644
--- a/src/cobra/io/sbml.py
+++ b/src/cobra/io/sbml.py
@@ -9,6 +9,7 @@
Parsing of fbc models was implemented as efficient as possible, whereas
(discouraged) fallback solutions are not optimized for efficiency.
+#TODO - fix the following paragraph, which is incorrect. Load up keyvalue pairs from notes??
Notes are only supported in a minimal way relevant for constraint-based
models. I.e., structured information from notes in the form
key: value
@@ -19,8 +20,6 @@
Annotations are read in the Object.annotation fields.
Some SBML related issues are still open, please refer to the respective issue:
-- update annotation format and support qualifiers (depends on decision
- for new annotation format; https://github.com/opencobra/cobrapy/issues/684)
- write compartment annotations and notes (depends on updated first-class
compartments; see https://github.com/opencobra/cobrapy/issues/760)
- support compression on file handles (depends on solution for
@@ -36,13 +35,27 @@
from copy import deepcopy
from io import StringIO
from sys import platform
-from typing import IO, Match, Optional, Pattern, Tuple, Type, Union
+from typing import IO, List, Match, Optional, Pattern, Tuple, Type, Union
+from warnings import warn
import libsbml
import cobra
-from ..core import GPR, Gene, Group, Metabolite, Model, Reaction
+from ..core import (
+ GPR,
+ Creator,
+ CVTerm,
+ CVTermList,
+ ExternalResources,
+ Gene,
+ Group,
+ Metabolite,
+ MetaData,
+ Model,
+ Reaction,
+)
+from ..core.metadata.history import STRTIME_FORMAT
from ..manipulation.validate import check_metabolite_compartment_formula
from ..util.solver import linear_reaction_coefficients, set_objective
@@ -600,40 +613,6 @@ def _sbml_to_model(
cobra_model = Model(model_id)
cobra_model.name = model.getName() or None
- # meta information
- meta = {
- "model.id": model_id,
- "level": model.getLevel(),
- "version": model.getVersion(),
- "packages": [],
- }
- # History
- creators = []
- created = None
- if model.isSetModelHistory():
- history: "libsbml.ModelHistory" = model.getModelHistory()
-
- if history.isSetCreatedDate():
- created = history.getCreatedDate()
-
- c: "libsbml.ModelCreator"
- for c in history.getListCreators():
- creators.append(
- {
- "familyName": c.getFamilyName() if c.isSetFamilyName() else None,
- "givenName": c.getGivenName() if c.isSetGivenName() else None,
- "organisation": c.getOrganisation()
- if c.isSetOrganisation()
- else None,
- "email": c.getEmail() if c.isSetEmail() else None,
- }
- )
-
- meta["creators"] = creators
- meta["created"] = created
- meta["notes"] = _parse_notes_dict(doc)
- meta["annotation"] = _parse_annotations(doc)
-
info = f"<{model_id}> SBML L{model.getLevel()}V{model.getVersion()}"
packages = {}
for k in range(doc.getNumPlugins()):
@@ -646,8 +625,17 @@ def _sbml_to_model(
f"SBML package '{key}' not supported by cobrapy, "
f"information is not parsed"
)
- meta["info"] = info
- meta["packages"] = packages
+
+ # meta information
+ meta = {
+ "model.id": model_id,
+ "level": model.getLevel(),
+ "version": model.getVersion(),
+ "packages": packages,
+ "notes": _parse_notes_dict(doc),
+ "annotation": _parse_annotations(doc),
+ "info": info,
+ }
cobra_model._sbml = meta
# notes and annotations
@@ -657,9 +645,8 @@ def _sbml_to_model(
# Compartments
# FIXME: update with new compartments
compartments = {}
- for (
- compartment
- ) in model.getListOfCompartments(): # noqa: E501 type: libsbml.Compartment
+ compartment: libsbml.Compartment
+ for compartment in model.getListOfCompartments():
cid = _check_required(compartment, compartment.getIdAttribute(), "id")
compartments[cid] = compartment.getName()
cobra_model.compartments = compartments
@@ -693,17 +680,16 @@ def _sbml_to_model(
f"discouraged, use fbc:charge instead: {specie}"
)
met.charge = specie.getCharge()
- else:
- if "CHARGE" in met.notes:
- LOGGER.warning(
- f"Use of CHARGE in the notes element is "
- f"discouraged, use fbc:charge instead: {specie}"
- )
- try:
- met.charge = int(met.notes["CHARGE"])
- except ValueError:
- # handle nan, na, NA, ...
- pass
+ elif "CHARGE" in met.notes:
+ LOGGER.warning(
+ f"Use of CHARGE in the notes element is "
+ f"discouraged, use fbc:charge instead: {specie}"
+ )
+ try:
+ met.charge = int(met.notes["CHARGE"])
+ except ValueError:
+ # handle nan, na, NA, ...
+ pass
if "FORMULA" in met.notes:
LOGGER.warning(
@@ -726,7 +712,7 @@ def _sbml_to_model(
ex_rid = f"EX_{met.id}"
ex_reaction = Reaction(ex_rid)
ex_reaction.name = ex_rid
- ex_reaction.annotation = {"sbo": SBO_EXCHANGE_REACTION}
+ ex_reaction.annotation = {"sbo": [SBO_EXCHANGE_REACTION]}
ex_reaction.lower_bound = config.lower_bound
ex_reaction.upper_bound = config.upper_bound
LOGGER.warning(
@@ -740,9 +726,8 @@ def _sbml_to_model(
# Genes
if model_fbc:
- for (
- gp
- ) in model_fbc.getListOfGeneProducts(): # noqa: E501 type: libsbml.GeneProduct
+ gp: "libsbml.GeneProduct"
+ for gp in model_fbc.getListOfGeneProducts():
gid = _check_required(gp, gp.getIdAttribute(), "id")
if f_replace and F_GENE in f_replace:
gid = f_replace[F_GENE](gid)
@@ -755,18 +740,11 @@ def _sbml_to_model(
cobra_model.genes.append(cobra_gene)
else:
- for (
- cobra_reaction
- ) in model.getListOfReactions(): # noqa: E501 type: libsbml.Reaction
+ cobra_reaction: "libsbml.Reaction"
+ for cobra_reaction in model.getListOfReactions():
# fallback to notes information
notes = _parse_notes_dict(cobra_reaction)
- if "GENE ASSOCIATION" in notes:
- gpr = notes["GENE ASSOCIATION"]
- elif "GENE_ASSOCIATION" in notes:
- gpr = notes["GENE_ASSOCIATION"]
- else:
- gpr = ""
-
+ gpr = notes.get("GENE ASSOCIATION", "") or notes.get("GENE_ASSOCIATION", "")
if len(gpr) > 0:
gpr = gpr.replace("(", ";")
gpr = gpr.replace(")", ";")
@@ -861,14 +839,10 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
elif reaction.isSetKineticLaw():
# some legacy models encode bounds in kinetic laws
klaw: "libsbml.KineticLaw" = reaction.getKineticLaw()
- p_lb = klaw.getParameter(
- "LOWER_BOUND"
- ) # noqa: E501 type: libsbml.LocalParameter
+ p_lb: "libsbml.LocalParameter" = klaw.getParameter("LOWER_BOUND")
if p_lb:
cobra_reaction.lower_bound = p_lb.getValue()
- p_ub = klaw.getParameter(
- "UPPER_BOUND"
- ) # noqa: E501 type: libsbml.LocalParameter
+ p_ub: "libsbml.LocalParameter" = klaw.getParameter("UPPER_BOUND")
if p_ub:
cobra_reaction.upper_bound = p_ub.getValue()
@@ -902,9 +876,8 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
# parse equation
stoichiometry = defaultdict(lambda: 0)
- for (
- sref
- ) in reaction.getListOfReactants(): # noqa: E501 type: libsbml.SpeciesReference
+ sref: "libsbml.SpeciesReference"
+ for sref in reaction.getListOfReactants():
sid = _check_required(sref, sref.getSpecies(), "species")
if f_replace and F_SPECIE in f_replace:
@@ -913,9 +886,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
_check_required(sref, sref.getStoichiometry(), "stoichiometry")
)
- for (
- sref
- ) in reaction.getListOfProducts(): # noqa: E501 type: libsbml.SpeciesReference
+ for sref in reaction.getListOfProducts():
sid = _check_required(sref, sref.getSpecies(), "species")
if f_replace and F_SPECIE in f_replace:
@@ -934,24 +905,15 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
# GPR
if r_fbc:
gpr = None
- gpa = (
- r_fbc.getGeneProductAssociation()
- ) # noqa: E501 type: libsbml.GeneProductAssociation
+ gpa: libsbml.GeneProductAssociation = r_fbc.getGeneProductAssociation()
if gpa is not None:
- association = (
- gpa.getAssociation()
- ) # noqa: E501 type: libsbml.FbcAssociation
+ association: libsbml.FbcAssociation = gpa.getAssociation()
gpr = Module(process_association(association))
cobra_reaction.gpr = GPR(gpr_from=gpr)
else:
# fallback to notes information
notes = cobra_reaction.notes
- if "GENE ASSOCIATION" in notes:
- gpr = notes["GENE ASSOCIATION"]
- elif "GENE_ASSOCIATION" in notes:
- gpr = notes["GENE_ASSOCIATION"]
- else:
- gpr = ""
+ gpr = notes.get("GENE ASSOCIATION", "") or notes.get("GENE_ASSOCIATION", "")
if len(gpr) > 0:
LOGGER.warning(
@@ -969,9 +931,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
obj_direction = "max"
coefficients = {}
if model_fbc:
- obj_list = (
- model_fbc.getListOfObjectives()
- ) # noqa: E501 type: libsbml.ListOfObjectives
+ obj_list: "libsbml.ListOfObjectives" = model_fbc.getListOfObjectives()
if obj_list is None:
LOGGER.warning("listOfObjectives element not found")
elif obj_list.size() == 0:
@@ -983,11 +943,8 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
obj: "libsbml.Objective" = model_fbc.getObjective(obj_id)
obj_direction = LONG_SHORT_DIRECTION[obj.getType()]
- for (
- flux_obj
- ) in (
- obj.getListOfFluxObjectives()
- ): # noqa: E501 type: libsbml.FluxObjective
+ flux_obj: "libsbml.FluxObjective"
+ for flux_obj in obj.getListOfFluxObjectives():
rid = flux_obj.getReaction()
if f_replace and F_REACTION in f_replace:
rid = f_replace[F_REACTION](rid)
@@ -1121,7 +1078,7 @@ def process_association(ass: "libsbml.FbcAssociation") -> Union[BoolOp, Name]:
if f_replace and F_GROUP in f_replace:
gid = f_replace[F_GROUP](gid)
cobra_group = Group(gid, name=gid, kind="partonomy")
- cobra_group.annotation["sbo"] = "SBO:0000633"
+ cobra_group.annotation["sbo"] = ["SBO:0000633"]
cobra_group.add_members(cobra_members)
groups.append(cobra_group)
@@ -1226,49 +1183,20 @@ def _model_to_sbml(
if cobra_model.name is not None:
model.setName(cobra_model.name)
- # for parsing annotation corresponding to the model
+ # for parsing annotation corresponding to the model, including model history
_sbase_annotations(model, cobra_model.annotation)
# for parsing notes corresponding to the model
_sbase_notes_dict(model, cobra_model.notes)
# Meta information (ModelHistory) related to SBMLDocument
- if hasattr(cobra_model, "_sbml"):
- meta = cobra_model._sbml
+ meta = getattr(cobra_model, "_sbml", None)
+ if meta:
if "annotation" in meta:
_sbase_annotations(doc, meta["annotation"])
+
if "notes" in meta:
_sbase_notes_dict(doc, meta["notes"])
- history: "libsbml.ModelHistory" = libsbml.ModelHistory()
- if "created" in meta and meta["created"]:
- history.setCreatedDate(meta["created"])
- else:
- time = datetime.datetime.now()
- timestr = time.strftime("%Y-%m-%dT%H:%M:%S")
- date = libsbml.Date(timestr)
- _check(history.setCreatedDate(date), "set creation date")
- _check(history.setModifiedDate(date), "set modified date")
-
- if "creators" in meta:
- for cobra_creator in meta[
- "creators"
- ]: # noqa: E501 type: libsbml.ModelCreator
- creator = libsbml.ModelCreator()
- if cobra_creator.get("familyName", None):
- creator.setFamilyName(cobra_creator["familyName"])
- if cobra_creator.get("givenName", None):
- creator.setGivenName(cobra_creator["givenName"])
- if cobra_creator.get("organisation", None):
- creator.setOrganisation(cobra_creator["organisation"])
- if cobra_creator.get("email", None):
- creator.setEmail(cobra_creator["email"])
-
- _check(history.addCreator(creator), "adding creator to ModelHistory.")
-
- # TODO: Will be implemented as part of
- # https://github.com/opencobra/cobrapy/issues/810
- # _check(model.setModelHistory(history), 'set model history')
-
# Units
flux_udef = None
if units:
@@ -1379,16 +1307,12 @@ def _model_to_sbml(
if f_replace and F_SPECIE_REV in f_replace:
sid = f_replace[F_SPECIE_REV](sid)
if stoichiometry < 0:
- sref = (
- reaction.createReactant()
- ) # noqa: E501 type: libsbml.SpeciesReference
+ sref: libsbml.SpeciesReference = reaction.createReactant()
sref.setSpecies(sid)
sref.setStoichiometry(-stoichiometry)
sref.setConstant(True)
else:
- sref = (
- reaction.createProduct()
- ) # noqa: E501 type: libsbml.SpeciesReference
+ sref: libsbml.SpeciesReference = reaction.createProduct()
sref.setSpecies(sid)
sref.setStoichiometry(stoichiometry)
sref.setConstant(True)
@@ -1426,18 +1350,14 @@ def _model_to_sbml(
else:
gpr_new = gpr.to_string()
- gpa = (
- r_fbc.createGeneProductAssociation()
- ) # noqa: E501 type: libsbml.GeneProductAssociation
+ gpa: libsbml.GeneProductAssociation = r_fbc.createGeneProductAssociation()
# uses ids to identify GeneProducts (True),
# does not create GeneProducts (False)
_check(gpa.setAssociation(gpr_new, True, False), "set gpr: " + gpr_new)
# objective coefficients
if reaction_coefficients.get(cobra_reaction, 0) != 0:
- flux_obj = (
- objective.createFluxObjective()
- ) # noqa: E501 type: libsbml.FluxObjective
+ flux_obj: libsbml.FluxObjective = objective.createFluxObjective()
flux_obj.setReaction(rid)
flux_obj.setCoefficient(cobra_reaction.objective_coefficient)
@@ -1447,9 +1367,7 @@ def _model_to_sbml(
"http://www.sbml.org/sbml/level3/version1/groups/version1", "groups", True
)
doc.setPackageRequired("groups", False)
- model_group = model.getPlugin(
- "groups"
- ) # noqa: E501 type: libsbml.GroupsModelPlugin
+ model_group: libsbml.GroupsModelPlugin = model.getPlugin("groups")
for cobra_group in cobra_model.groups:
group: "libsbml.Group" = model_group.createGroup()
if f_replace and F_GROUP_REV in f_replace:
@@ -1469,15 +1387,12 @@ def _model_to_sbml(
m_type = str(type(cobra_member))
# id replacements
- if "Reaction" in m_type:
- if f_replace and F_REACTION_REV in f_replace:
- mid = f_replace[F_REACTION_REV](mid)
- if "Metabolite" in m_type:
- if f_replace and F_SPECIE_REV in f_replace:
- mid = f_replace[F_SPECIE_REV](mid)
- if "Gene" in m_type:
- if f_replace and F_GENE_REV in f_replace:
- mid = f_replace[F_GENE_REV](mid)
+ if "Reaction" in m_type and f_replace and F_REACTION_REV in f_replace:
+ mid = f_replace[F_REACTION_REV](mid)
+ if "Metabolite" in m_type and f_replace and F_SPECIE_REV in f_replace:
+ mid = f_replace[F_SPECIE_REV](mid)
+ if "Gene" in m_type and f_replace and F_GENE_REV in f_replace:
+ mid = f_replace[F_GENE_REV](mid)
member.setIdRef(mid)
if cobra_member.name and len(cobra_member.name) > 0:
@@ -1733,21 +1648,21 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None:
URL_IDENTIFIERS_PATTERN = re.compile(r"^https?://identifiers.org/(.+?)[:/](.+)")
URL_IDENTIFIERS_PREFIX = "https://identifiers.org"
-QUALIFIER_TYPES = {
- "is": libsbml.BQB_IS,
- "hasPart": libsbml.BQB_HAS_PART,
- "isPartOf": libsbml.BQB_IS_PART_OF,
- "isVersionOf": libsbml.BQB_IS_VERSION_OF,
- "hasVersion": libsbml.BQB_HAS_VERSION,
- "isHomologTo": libsbml.BQB_IS_HOMOLOG_TO,
- "isDescribedBy": libsbml.BQB_IS_DESCRIBED_BY,
- "isEncodedBy": libsbml.BQB_IS_ENCODED_BY,
- "encodes": libsbml.BQB_ENCODES,
- "occursIn": libsbml.BQB_OCCURS_IN,
- "hasProperty": libsbml.BQB_HAS_PROPERTY,
- "isPropertyOf": libsbml.BQB_IS_PROPERTY_OF,
- "hasTaxon": libsbml.BQB_HAS_TAXON,
- "unknown": libsbml.BQB_UNKNOWN,
+QUALIFIER_TYPES_COBRA_SBML_DICT = {
+ "bqb_is": libsbml.BQB_IS,
+ "bqb_hasPart": libsbml.BQB_HAS_PART,
+ "bqb_isPartOf": libsbml.BQB_IS_PART_OF,
+ "bqb_isVersionOf": libsbml.BQB_IS_VERSION_OF,
+ "bqb_hasVersion": libsbml.BQB_HAS_VERSION,
+ "bqb_isHomologTo": libsbml.BQB_IS_HOMOLOG_TO,
+ "bqb_isDescribedBy": libsbml.BQB_IS_DESCRIBED_BY,
+ "bqb_isEncodedBy": libsbml.BQB_IS_ENCODED_BY,
+ "bqb_encodes": libsbml.BQB_ENCODES,
+ "bqb_occursIn": libsbml.BQB_OCCURS_IN,
+ "bqb_hasProperty": libsbml.BQB_HAS_PROPERTY,
+ "bqb_isPropertyOf": libsbml.BQB_IS_PROPERTY_OF,
+ "bqb_hasTaxon": libsbml.BQB_HAS_TAXON,
+ "bqb_unknown": libsbml.BQB_UNKNOWN,
"bqm_is": libsbml.BQM_IS,
"bqm_isDescribedBy": libsbml.BQM_IS_DESCRIBED_BY,
"bqm_isDerivedFrom": libsbml.BQM_IS_DERIVED_FROM,
@@ -1755,12 +1670,33 @@ def _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) -> None:
"bqm_hasInstance": libsbml.BQM_HAS_INSTANCE,
"bqm_unknown": libsbml.BQM_UNKNOWN,
}
+BIOLOGY_QUALIFIER_TYPES_TO_COBRA_DICT = {
+ value: key
+ for key, value in QUALIFIER_TYPES_COBRA_SBML_DICT.items()
+ if re.match("bqb", key)
+}
+MODEL_QUALIFIER_TYPES_TO_COBRA_DICT = {
+ value: key
+ for key, value in QUALIFIER_TYPES_COBRA_SBML_DICT.items()
+ if re.match("bqm", key)
+}
-def _parse_annotations(sbase: libsbml.SBase) -> dict:
+def _parse_annotations(sbase: libsbml.SBase) -> MetaData:
"""Parse cobra annotations from a given SBase object.
- Annotations are dictionaries with the providers as keys.
+ The annotation format has been changed. We no longer have
+ simple dictionaries for storing annotation data. Dedicated
+ classes for storing CVTerm data, History data and key-value
+ pair data corresponding to an SBase object have been made.
+ The metadata classes inside cobra.core directory contains
+ of them. All the existing issues in old annotation format have
+ been solved. The new format annotation is completely backward
+ compatible. It can read models with old annotation format,
+ can convert old format annotation to new format annotation,
+ and writes annotation in new format only (for JSON and other
+ formats). The JSON schema v2 specifies the new format annotation
+ whereas JSON schema v1 have annotation data defined in old format.
Parameters
----------
@@ -1769,15 +1705,13 @@ def _parse_annotations(sbase: libsbml.SBase) -> dict:
Returns
-------
- dict (annotation dictionary)
+ MetaData
+ a metadata object storing COBRA annotation
"""
- # FIXME: annotation format must be updated (this is a big collection of
- # fixes) - see: https://github.com/opencobra/cobrapy/issues/684)
- annotation = {}
+ annotation = MetaData()
# SBO term
if sbase.isSetSBOTerm():
- # FIXME: correct handling of annotations
annotation["sbo"] = sbase.getSBOTermID()
# RDF annotation
@@ -1785,27 +1719,76 @@ def _parse_annotations(sbase: libsbml.SBase) -> dict:
if cvterms is None:
return annotation
- cvterm: "libsbml.CVTerm"
- for cvterm in cvterms:
- for k in range(cvterm.getNumResources()):
- # FIXME: read and store the qualifier
+ def _cvterm_to_cobra(_cvterm: "libsbml.CVTerm") -> Optional[CVTerm]:
+ """Parse the libsbml.CVTerm object to cobra CVTerm.
- uri = cvterm.getResourceURI(k)
- data = _parse_annotation_info(uri)
- if data is None:
- continue
- else:
- provider, identifier = data
-
- if provider in annotation:
- if isinstance(annotation[provider], str):
- annotation[provider] = [annotation[provider]]
- # FIXME: use a list
- if identifier not in annotation[provider]:
- annotation[provider].append(identifier)
- else:
- # FIXME: always in list
- annotation[provider] = identifier
+ Parameters
+ ----------
+ _cvterm : libsbml.CVTerm
+ The libsbml.CVTerm object from which data is to be parsed.
+
+ Returns
+ -------
+ CVTerm or None
+ The parsed data of the given libsbml.CVTerm object as CVTerm.
+ If the qualifier is unknown, this function will return None.
+ """
+ qualifier_type = _cvterm.getQualifierType()
+ if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER:
+ qualifier = BIOLOGY_QUALIFIER_TYPES_TO_COBRA_DICT[
+ _cvterm.getBiologicalQualifierType()
+ ]
+ elif qualifier_type == libsbml.MODEL_QUALIFIER:
+ qualifier = MODEL_QUALIFIER_TYPES_TO_COBRA_DICT[
+ _cvterm.getModelQualifierType()
+ ]
+ else:
+ LOGGER.warning(f"The cvterm {_cvterm} has an unkown qualifier. Ignoring it")
+ return None
+ ext_res = {
+ "resources": [
+ _cvterm.getResourceURI(k) for k in range(_cvterm.getNumResources())
+ ]
+ }
+
+ nested_cv_terms = [
+ _cvterm.getNestedCVTerm(index)
+ for index in range(_cvterm.getNumNestedCVTerms())
+ ]
+ # This kludge is necessary since _cvterm.getListNestedCVTerms() doesn't give a
+ # python list, but a Swig List_t * and then SwigPyObject is not iterable
+ ext_res["nested_data"] = CVTermList(
+ [
+ _cvterm_to_cobra(_nested_cvterm)
+ for _nested_cvterm in nested_cv_terms
+ if _nested_cvterm
+ ]
+ )
+ return CVTerm(ExternalResources.from_dict(ext_res), qualifier)
+
+ annotation.add_cvterms([_cvterm_to_cobra(cvterm) for cvterm in cvterms if cvterm])
+
+ # history of the component
+ if sbase.isSetModelHistory():
+ model_history: "libsbml.ModelHistory" = sbase.getModelHistory()
+
+ annotation.history.creators = [
+ Creator(
+ creator.getGivenName() or None,
+ creator.getFamilyName() or None,
+ creator.getEmail() or None,
+ creator.getOrganisation() or None,
+ )
+ for creator in model_history.getListCreators()
+ ]
+
+ if model_history.isSetCreatedDate():
+ date: libsbml.Date = model_history.getCreatedDate()
+ annotation.history.created_date = date.getDateAsString()
+
+ annotation.history.modified_dates = [
+ _date.getDateAsString() for _date in model_history.getListModifiedDates()
+ ]
return annotation
@@ -1821,7 +1804,15 @@ def _parse_annotation_info(uri: str) -> Union[None, Tuple[str, str]]:
Returns
-------
(provider, identifier) if resolvable, None otherwise
+
+ .. deprecated ::
+ Use cobra.core.metadata.helper.parse_identifiers_uri()
"""
+ warn(
+ "_parse_annotation_info() is being replaced by "
+ "cobra.core.metadata.helper.parse_identifiers_uri()",
+ DeprecationWarning,
+ )
match = URL_IDENTIFIERS_PATTERN.match(uri)
if match:
provider, identifier = match.group(1), match.group(2)
@@ -1839,7 +1830,53 @@ def _parse_annotation_info(uri: str) -> Union[None, Tuple[str, str]]:
return provider, identifier
-def _sbase_annotations(sbase: libsbml.SBase, annotation: dict) -> None:
+def _cvterms_to_sbml(cvterms: CVTermList) -> List["libsbml.CVTerm"]:
+ """Convert cobra CVTerms to libsbml.CVTerm list.
+
+ Parameters
+ ----------
+ cvterms: CVTermList
+ cobra CVTerms object
+
+ Returns
+ -------
+ list
+ List of libsbml.cvTerm objects
+ """
+ cv_list = []
+ for cvterm in cvterms:
+ qualifier = cvterm.qualifier
+ if qualifier.name.startswith("bqb"):
+ qualifier_type = libsbml.BIOLOGICAL_QUALIFIER
+ elif qualifier.name.startswith("bqm"):
+ qualifier_type = libsbml.MODEL_QUALIFIER
+ else:
+ raise CobraSBMLError(f"Unsupported qualifier: {qualifier}")
+
+ cv: "libsbml.CVTerm" = libsbml.CVTerm()
+ cv.setQualifierType(qualifier_type)
+ if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER:
+ cv.setBiologicalQualifierType(
+ QUALIFIER_TYPES_COBRA_SBML_DICT[qualifier.name]
+ )
+ elif qualifier_type == libsbml.MODEL_QUALIFIER:
+ cv.setModelQualifierType(QUALIFIER_TYPES_COBRA_SBML_DICT[qualifier.name])
+ else:
+ raise CobraSBMLError(f"Unsupported qualifier: {qualifier}")
+ for uri in sorted(cvterm.external_resources.resources):
+ cv.addResource(uri)
+
+ [
+ _check(cv.addNestedCVTerm(_cv), f"Adding nested cvterm: {_cv}")
+ for _cv in _cvterms_to_sbml(cvterm.external_resources.nested_data)
+ ]
+
+ cv_list.append(cv)
+
+ return cv_list
+
+
+def _sbase_annotations(sbase: libsbml.SBase, annotation: MetaData) -> None:
"""Set SBase annotations based on cobra annotations.
Parameters
@@ -1853,73 +1890,78 @@ def _sbase_annotations(sbase: libsbml.SBase, annotation: dict) -> None:
------
CobraSBMLError for unsupported qualifier
"""
- # FIXME: annotation format must be updated
- # (https://github.com/opencobra/cobrapy/issues/684)
- if not annotation or len(annotation) == 0:
- return
-
- # standardize annotations
annotation_data = deepcopy(annotation)
- for key, value in annotation_data.items():
- # handling of non-string annotations (e.g. integers)
- if isinstance(value, (float, int)):
- value = str(value)
- if isinstance(value, str):
- annotation_data[key] = [("is", value)]
+ if not isinstance(annotation_data, MetaData):
+ raise TypeError(
+ f"The annotation object must be of type 'Metadata': {annotation_data}"
+ )
+
+ if "SBO" in annotation_data:
+ LOGGER.warning(
+ "'SBO' provider is deprecated, use 'sbo' provider instead. Converting to"
+ "'sbo' for writing."
+ )
+ annotation_data["sbo"] = annotation_data.pop("SBO")
- for _key, value in annotation_data.items():
- for idx, item in enumerate(value):
- if isinstance(item, str):
- value[idx] = ("is", item)
+ if "sbo" in annotation and annotation.sbo:
+ sbo_term = annotation_data.sbo
+ if isinstance(sbo_term, list):
+ sbo_term = sbo_term[0]
+ _check(sbase.setSBOTerm(sbo_term), f"Setting SBOTerm: {sbo_term}")
# set metaId
meta_id = f"meta_{sbase.getId()}"
sbase.setMetaId(meta_id)
- # rdf_items = []
- for provider, data in annotation_data.items():
+ # set standardized
+ [
+ # Question for @matthiaskoenig - should I be using createCVTerms?
+ _check(sbase.addCVTerm(cv, newBag=True), f"Setting cvterm: {cv}")
+ for cv in _cvterms_to_sbml(annotation.standardized)
+ ]
+
+ # set history
+ if not annotation.history.is_empty():
+ comp_history = libsbml.ModelHistory()
+
+ for creator in annotation.history.creators:
+ comp_creator = libsbml.ModelCreator()
+ comp_creator.setGivenName(creator.given_name)
+ comp_creator.setFamilyName(creator.family_name)
+ creator.email and comp_creator.setEmail(creator.email)
+ creator.organisation and comp_creator.setOrganisation(creator.organisation)
+ _check(
+ comp_history.addCreator(comp_creator),
+ f"adding creator to {sbase.getId}.",
+ )
- # set SBOTerm
- if provider in ["SBO", "sbo"]:
- if provider == "SBO":
- LOGGER.warning(
- "'SBO' provider is deprecated, use 'sbo' provider instead"
- )
- sbo_term = data[0][1]
- _check(sbase.setSBOTerm(sbo_term), f"Setting SBOTerm: {sbo_term}")
-
- # FIXME: sbo should also be written as CVTerm
- continue
-
- for item in data:
- qualifier_str, entity = item[0], item[1]
- qualifier = QUALIFIER_TYPES.get(qualifier_str, None)
- if qualifier is None:
- qualifier = libsbml.BQB_IS
- LOGGER.error(
- f"Qualifier type is not supported on annotation: '{qualifier_str}'"
- )
+ if annotation.history.created_date:
+ date = libsbml.Date(
+ annotation.history.created_date.strftime(STRTIME_FORMAT)
+ )
+ _check(
+ comp_history.setCreatedDate(date), f"set creation date for {sbase.id}"
+ )
+ elif isinstance(sbase, libsbml.SBMLDocument):
+ time = datetime.datetime.now()
+ timestr = time.strftime(STRTIME_FORMAT)
+ date = libsbml.Date(timestr)
+ _check(comp_history.setCreatedDate(date), "set creation date for document")
- qualifier_type = libsbml.BIOLOGICAL_QUALIFIER
- if qualifier_str.startswith("bqm_"):
- qualifier_type = libsbml.MODEL_QUALIFIER
-
- cv: "libsbml.CVTerm" = libsbml.CVTerm()
- cv.setQualifierType(qualifier_type)
- if qualifier_type == libsbml.BIOLOGICAL_QUALIFIER:
- cv.setBiologicalQualifierType(qualifier)
- elif qualifier_type == libsbml.MODEL_QUALIFIER:
- cv.setModelQualifierType(qualifier)
- else:
- raise CobraSBMLError(f"Unsupported qualifier: {qualifier}")
- resource = f"{URL_IDENTIFIERS_PREFIX}/{provider}/{entity}"
- cv.addResource(resource)
+ for modified_date in annotation.history.modified_dates:
+ date = libsbml.Date(modified_date.strftime(STRTIME_FORMAT))
_check(
- sbase.addCVTerm(cv),
- f"Setting cvterm: {cv}, resource: {resource}",
+ comp_history.addModifiedDate(date),
+ f"add modification date for {sbase.id}",
)
+ # finally add the compo_history
+ _check(
+ sbase.setModelHistory(comp_history),
+ f"Setting ModelHistory: {comp_history}",
+ )
+
# -----------------------------------------------------------------------------
# Validation
@@ -1965,17 +2007,30 @@ def validate_sbml_model(
from the libsbml validator. COBRA_* types are from the cobrapy SBML
parser.
"""
- keys = (
- "SBML_FATAL",
- "SBML_ERROR",
- "SBML_SCHEMA_ERROR",
- "SBML_WARNING",
- "COBRA_FATAL",
- "COBRA_ERROR",
- "COBRA_WARNING",
- "COBRA_CHECK",
- )
- errors = {key: [] for key in keys}
+ cobra_sbml_error_dict = {
+ "SBML_FATAL": libsbml.LIBSBML_SEV_FATAL,
+ "SBML_ERROR": libsbml.LIBSBML_SEV_ERROR,
+ "SBML_SCHEMA_ERROR": libsbml.LIBSBML_SEV_SCHEMA_ERROR,
+ "SBML_WARNING": libsbml.LIBSBML_SEV_WARNING,
+ "COBRA_FATAL": None,
+ "COBRA_ERROR": None,
+ "COBRA_WARNING": None,
+ "COBRA_CHECK": None,
+ }
+ sbml_severity_dict = {
+ value: key for key, value in cobra_sbml_error_dict.items() if value
+ }
+ errors = {key: [] for key in cobra_sbml_error_dict.keys()}
+ sbml_log_dict = {
+ "SBML_FATAL": "SBML errors",
+ "SBML_ERROR": "SBML errors",
+ "SBML_SCHEMA_ERROR": "SBML errors",
+ "SBML_WARNING": "SBML warnings",
+ "COBRA_FATAL": "COBRA errors",
+ "COBRA_ERROR": "COBRA errors",
+ "COBRA_WARNING": "COBRA warnings",
+ "COBRA_CHECK": "COBRA warnings",
+ }
# [1] libsbml validation
doc: "libsbml.SBMLDocument" = _get_doc_from_filename(filename)
@@ -1997,14 +2052,7 @@ def validate_sbml_model(
e: "libsbml.SBMLError" = doc.getError(k)
msg = _error_string(e, k=k)
sev = e.getSeverity()
- if sev == libsbml.LIBSBML_SEV_FATAL:
- errors["SBML_FATAL"].append(msg)
- elif sev == libsbml.LIBSBML_SEV_ERROR:
- errors["SBML_ERROR"].append(msg)
- elif sev == libsbml.LIBSBML_SEV_SCHEMA_ERROR:
- errors["SBML_SCHEMA_ERROR"].append(msg)
- elif sev == libsbml.LIBSBML_SEV_WARNING:
- errors["SBML_WARNING"].append(msg)
+ errors[sbml_severity_dict[sev]].append(msg)
# [2] cobrapy validation (check that SBML can be read into model)
# all warnings generated while loading will be logged as errors
@@ -2021,10 +2069,10 @@ def validate_sbml_model(
model = _sbml_to_model(doc, **kwargs)
except CobraSBMLError as e:
errors["COBRA_ERROR"].append(str(e))
- return None, errors
+ model = None # If we return, we won't get to the errors["COBRA_ERROR"]
except Exception as e:
errors["COBRA_FATAL"].append(str(e))
- return None, errors
+ model = None
cobra_errors = log_stream.getvalue().split("\n")
for cobra_error in cobra_errors:
@@ -2045,21 +2093,11 @@ def validate_sbml_model(
if check_model:
errors["COBRA_CHECK"].extend(check_metabolite_compartment_formula(model))
- for key in ["SBML_FATAL", "SBML_ERROR", "SBML_SCHEMA_ERROR"]:
- if len(errors[key]) > 0:
- LOGGER.error("SBML errors in validation, check error log for details.")
- break
- for key in ["SBML_WARNING"]:
+ for key in sbml_log_dict.keys():
if len(errors[key]) > 0:
- LOGGER.error("SBML warnings in validation, check error log for details.")
- break
- for key in ["COBRA_FATAL", "COBRA_ERROR"]:
- if len(errors[key]) > 0:
- LOGGER.error("COBRA errors in validation, check error log for details.")
- break
- for key in ["COBRA_WARNING", "COBRA_CHECK"]:
- if len(errors[key]) > 0:
- LOGGER.error("COBRA warnings in validation, check error log for details.")
+ LOGGER.error(
+ f"{sbml_log_dict[key]} in validation, check error log for details."
+ )
break
return model, errors
diff --git a/src/cobra/io/schema_v1.json b/src/cobra/io/schema_v1.json
index edc9756fb..8fd7cb0a4 100644
--- a/src/cobra/io/schema_v1.json
+++ b/src/cobra/io/schema_v1.json
@@ -153,5 +153,5 @@
"metabolites",
"genes"
],
- "additionalProperties": false
+ "additionalProperties": true
}
diff --git a/src/cobra/io/schema_v2.json b/src/cobra/io/schema_v2.json
new file mode 100644
index 000000000..2aaadfbe9
--- /dev/null
+++ b/src/cobra/io/schema_v2.json
@@ -0,0 +1,370 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "title": "COBRA",
+ "description": "JSON representation of COBRA model",
+ "definitions": {
+ "annotation": {
+ "type": "object",
+ "properties": {
+ "sbo": {
+ "type": "string"
+ },
+ "cvterms": {
+ "type": "object",
+ "additionalProperties": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "resources": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ }
+ },
+ "nested_data": {
+ "$ref": "#/definitions/annotation"
+ }
+ }
+ }
+ }
+ },
+ "history": {
+ "type": "object",
+ "properties": {
+ "creators": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "email": {
+ "type": "string"
+ },
+ "given_name": {
+ "type": "string"
+ },
+ "family_name": {
+ "type": "string"
+ },
+ "organisation": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "given_name",
+ "family_name"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "created_date": {
+ "type": "string",
+ "format": "date-time"
+ },
+ "modified_dates": {
+ "type": "array",
+ "items": {
+ "type": "string",
+ "format": "date-time"
+ }
+ }
+ },
+ "required": [
+ "creators",
+ "created_date",
+ "modified_dates"
+ ],
+ "additionalProperties": false
+ },
+ "listofkeyvalue": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "key": {
+ "type": "string"
+ },
+ "value": {
+ "type": "string"
+ },
+ "uri": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "key"
+ ],
+ "additionalProperties": false
+ }
+ }
+ }
+ }
+ },
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "version": {
+ "type": "string",
+ "default": "1"
+ },
+ "reactions": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "metabolites": {
+ "type": "object",
+ "patternProperties": {
+ ".*": {
+ "type": "number"
+ }
+ }
+ },
+ "gene_reaction_rule": {
+ "type": "string"
+ },
+ "lower_bound": {
+ "type": "number"
+ },
+ "upper_bound": {
+ "type": "number"
+ },
+ "objective_coefficient": {
+ "type": "number",
+ "default": 0
+ },
+ "subsystem": {
+ "type": "string"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ }
+ },
+ "required": [
+ "id",
+ "name",
+ "metabolites",
+ "lower_bound",
+ "upper_bound",
+ "gene_reaction_rule"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "metabolites": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "compartment": {
+ "type": "string",
+ "pattern": "[a-z]{1,2}"
+ },
+ "charge": {
+ "type": "integer"
+ },
+ "formula": {
+ "type": "string"
+ },
+ "_bound": {
+ "type": "number",
+ "default": 0
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ }
+ },
+ "required": [
+ "id",
+ "name",
+ "compartment"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "genes": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ }
+ },
+ "required": [
+ "id",
+ "name"
+ ],
+ "additionalProperties": false
+ }
+ },
+ "compartments": {
+ "type": "object",
+ "patternProperties": {
+ "[a-z]{1,2}": {
+ "type": "string"
+ }
+ }
+ },
+ "groups": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ },
+ "kind": {
+ "type": "string",
+ "enum": ["collection", "classification", "partonomy"]
+ },
+ "members": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "idRef": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "type": {
+ "type": "string"
+ }
+ },
+ "required": ["idRef", "type"]
+ }
+ }
+ },
+ "required": ["kind", "members"]
+ }
+ },
+ "user_defined_constraints": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "lower_bound": {
+ "type": "number"
+ },
+ "upper_bound": {
+ "type": "number"
+ },
+ "constraint_comps": {
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "id": {
+ "type": "string",
+ "pattern": "^[a-zA-Z|_][a-zA-Z0-9_]*$"
+ },
+ "name": {
+ "type": "string"
+ },
+ "coefficient": {
+ "type": "number"
+ },
+ "variable": {
+ "type": "string"
+ },
+ "variable_type": {
+ "type": "string",
+ "enum": ["linear", "quadratic"]
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ }
+ },
+ "required": ["variable"],
+ "additionalProperties": false
+ }
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ }
+ },
+ "required": ["lower_bound", "upper_bound", "constraint_comps"],
+ "additionalProperties": false
+ }
+ },
+ "notes": {
+ "type": "string"
+ },
+ "annotation": {
+ "$ref": "#/definitions/annotation"
+ }
+ },
+ "required": [
+ "id",
+ "reactions",
+ "metabolites",
+ "genes"
+ ],
+ "additionalProperties": true
+}
diff --git a/src/cobra/manipulation/annotate.py b/src/cobra/manipulation/annotate.py
index 6f989dd2a..9bad70d41 100644
--- a/src/cobra/manipulation/annotate.py
+++ b/src/cobra/manipulation/annotate.py
@@ -22,15 +22,18 @@ def add_SBO(model: "Model") -> None:
The model whose demand and exchange reactions need to be annotated.
"""
+ # ??? Should this be done with boundary?
for r in model.reactions:
# don't annotate already annotated reactions
- if r.annotation.get("sbo"):
+ if len(r.annotation.get("sbo")) != 0 and r.annotation.sbo:
continue
# only doing exchanges
if len(r.metabolites) != 1:
continue
met_id = list(r._metabolites)[0].id
if r.id.startswith("EX_") and r.id == "EX_" + met_id:
- r.annotation["sbo"] = "SBO:0000627"
+ r.annotation["sbo"] = ["SBO:0000627"]
elif r.id.startswith("DM_") and r.id == "DM_" + met_id:
- r.annotation["sbo"] = "SBO:0000628"
+ r.annotation["sbo"] = ["SBO:0000628"]
+ elif r.id.startswith("SK_") and r.id == "SK_" + met_id:
+ r.annotation["sbo"] = ["SBO:0000632"]
diff --git a/src/cobra/manipulation/validate.py b/src/cobra/manipulation/validate.py
index 344a05437..34c821690 100644
--- a/src/cobra/manipulation/validate.py
+++ b/src/cobra/manipulation/validate.py
@@ -33,7 +33,7 @@ def check_mass_balance(model: "Model") -> Dict["Reaction", Dict["Metabolite", fl
"""
unbalanced = {}
for reaction in model.reactions:
- if reaction.annotation.get("sbo") not in _NOT_MASS_BALANCED_TERMS:
+ if set(reaction.annotation.get("sbo", [])).isdisjoint(_NOT_MASS_BALANCED_TERMS):
balance = reaction.check_mass_balance()
if balance:
unbalanced[reaction] = balance
diff --git a/src/cobra/medium/boundary_types.py b/src/cobra/medium/boundary_types.py
index 0229b4bb4..2b327d82a 100644
--- a/src/cobra/medium/boundary_types.py
+++ b/src/cobra/medium/boundary_types.py
@@ -125,9 +125,9 @@ def is_boundary_type(
"""
# Check if the reaction has an annotation. Annotations dominate everything.
sbo_term = reaction.annotation.get("sbo", "")
- if isinstance(sbo_term, list):
+ if isinstance(sbo_term, list) and len(sbo_term) != 0:
sbo_term = sbo_term[0]
- sbo_term = sbo_term.upper()
+ sbo_term = sbo_term.upper()
if sbo_term == sbo_terms[boundary_type]:
return True
diff --git a/tests/conftest.py b/tests/conftest.py
index 0833f6d55..06792bba0 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -20,7 +20,7 @@ def create_test_model(model_name: str = "salmonella") -> Model:
Parameters
----------
model_name: str
- One of 'ecoli', 'textbook', or 'salmonella', or the
+ One of 'ecoli', 'textbook', or 'salmonella', 'ecoli_annotation' or the
path to a pickled cobra.Model .
Returns
@@ -43,6 +43,9 @@ def create_test_model(model_name: str = "salmonella") -> Model:
elif model_name == "mini":
mini_sbml = str((data_dir / "mini_fbc2.xml").resolve())
return read_sbml_model(mini_sbml)
+ elif model_name == "ecoli_annotation":
+ ecoli_annotation_sbml = str((data_dir / "e_coli_core_for_annotation.xml").resolve())
+ return read_sbml_model(ecoli_annotation_sbml)
elif model_name == "salmonella":
salmonella_pickle = str((data_dir / "salmonella.pickle").resolve())
model_name = salmonella_pickle
@@ -104,6 +107,18 @@ def salmonella(medium_model: Model) -> Model:
return medium_model.copy()
+@pytest.fixture(scope="session")
+def ecoli_annotation_model() -> Model:
+ """Provide session-level fixture for ecoli_annotation model."""
+ return create_test_model("ecoli_annotation")
+
+
+@pytest.fixture(scope="function")
+def annotation_model(ecoli_annotation_model: Model) -> Model:
+ """Provide function-level fixture for ecoli_annotation model."""
+ return ecoli_annotation_model.copy()
+
+
@pytest.fixture(scope="function")
def solved_model(data_directory: Path) -> Tuple[Solution, Model]:
"""Provide function-level fixture for solved textbook model."""
diff --git a/tests/data/cvterms_nested.json b/tests/data/cvterms_nested.json
new file mode 100644
index 000000000..e6f169c78
--- /dev/null
+++ b/tests/data/cvterms_nested.json
@@ -0,0 +1,33 @@
+[
+ {
+ "external_resources": {
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://identifiers.org/uniprot/P68871",
+ "https://identifiers.org/kegg.compound/C00032"
+ ]
+ },
+ "qualifier": "bqb_hasPart"
+ },
+ {
+ "qualifier": "bqb_hasPart",
+ "external_resources": {
+ "resources": [
+ "https://identifiers.org/uniprot/P69905",
+ "https://www.uniprot.org/uniprot/P68871",
+ "https://identifiers.org/chebi/CHEBI:17627"
+ ],
+ "nested_data": [
+ {
+ "qualifier": "bqb_isDescribedBy",
+ "external_resources": {
+ "resources": [
+ "https://identifiers.org/pubmed/1111111",
+ "https://identifiers.org/eco/000000"
+ ]
+ }
+ }
+ ]
+ }
+ }
+]
diff --git a/tests/data/e_coli_core.json b/tests/data/e_coli_core.json
new file mode 100644
index 000000000..39db77321
--- /dev/null
+++ b/tests/data/e_coli_core.json
@@ -0,0 +1,14786 @@
+{
+"metabolites":[
+{
+"id":"glc__D_e",
+"name":"D-Glucose",
+"compartment":"e",
+"charge":0,
+"formula":"C6H12O6",
+"notes":{
+"original_bigg_ids":[
+"glc_D_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glc__D"
+],
+"biocyc":[
+"META:Glucopyranose"
+],
+"chebi":[
+"CHEBI:12965",
+"CHEBI:20999",
+"CHEBI:4167",
+"CHEBI:17634"
+],
+"hmdb":[
+"HMDB00122",
+"HMDB06564"
+],
+"inchi_key":[
+"WQZGKKKJIJFFOK-GASJEMHNSA-N"
+],
+"kegg.compound":[
+"C00031"
+],
+"kegg.drug":[
+"D00009"
+],
+"metanetx.chemical":[
+"MNXM41"
+],
+"sabiork":[
+"1406",
+"1407"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd26821",
+"cpd00027"
+]
+}
+},
+{
+"id":"gln__L_c",
+"name":"L-Glutamine",
+"compartment":"c",
+"charge":0,
+"formula":"C5H10N2O3",
+"notes":{
+"original_bigg_ids":[
+"gln_L_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"gln__L"
+],
+"biocyc":[
+"META:GLN"
+],
+"chebi":[
+"CHEBI:42943",
+"CHEBI:42899",
+"CHEBI:32679",
+"CHEBI:32678",
+"CHEBI:58359",
+"CHEBI:28300",
+"CHEBI:42812",
+"CHEBI:13110",
+"CHEBI:18050",
+"CHEBI:32666",
+"CHEBI:6227",
+"CHEBI:32665",
+"CHEBI:21308",
+"CHEBI:42814",
+"CHEBI:5432",
+"CHEBI:24316"
+],
+"hmdb":[
+"HMDB00641"
+],
+"inchi_key":[
+"ZDXPYRJPNDTMRX-VKHMYHEASA-N"
+],
+"kegg.compound":[
+"C00064",
+"C00303"
+],
+"kegg.drug":[
+"D00015"
+],
+"metanetx.chemical":[
+"MNXM37"
+],
+"reactome.compound":[
+"113522",
+"212615",
+"29472"
+],
+"sabiork":[
+"2011",
+"74"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00253",
+"cpd00053"
+]
+}
+},
+{
+"id":"gln__L_e",
+"name":"L-Glutamine",
+"compartment":"e",
+"charge":0,
+"formula":"C5H10N2O3",
+"notes":{
+"original_bigg_ids":[
+"gln_L_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"gln__L"
+],
+"biocyc":[
+"META:GLN"
+],
+"chebi":[
+"CHEBI:42943",
+"CHEBI:42899",
+"CHEBI:32679",
+"CHEBI:32678",
+"CHEBI:58359",
+"CHEBI:28300",
+"CHEBI:42812",
+"CHEBI:13110",
+"CHEBI:18050",
+"CHEBI:32666",
+"CHEBI:6227",
+"CHEBI:32665",
+"CHEBI:21308",
+"CHEBI:42814",
+"CHEBI:5432",
+"CHEBI:24316"
+],
+"hmdb":[
+"HMDB00641"
+],
+"inchi_key":[
+"ZDXPYRJPNDTMRX-VKHMYHEASA-N"
+],
+"kegg.compound":[
+"C00064",
+"C00303"
+],
+"kegg.drug":[
+"D00015"
+],
+"metanetx.chemical":[
+"MNXM37"
+],
+"reactome.compound":[
+"113522",
+"212615",
+"29472"
+],
+"sabiork":[
+"2011",
+"74"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00253",
+"cpd00053"
+]
+}
+},
+{
+"id":"glu__L_c",
+"name":"L-Glutamate",
+"compartment":"c",
+"charge":-1,
+"formula":"C5H8NO4",
+"notes":{
+"original_bigg_ids":[
+"glu_L_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glu__L"
+],
+"biocyc":[
+"META:Glutamates",
+"META:GLT"
+],
+"chebi":[
+"CHEBI:76051",
+"CHEBI:21301",
+"CHEBI:29985",
+"CHEBI:42825",
+"CHEBI:29987",
+"CHEBI:18237",
+"CHEBI:24314",
+"CHEBI:16015",
+"CHEBI:13107",
+"CHEBI:5431",
+"CHEBI:21304",
+"CHEBI:6224",
+"CHEBI:14321",
+"CHEBI:29988"
+],
+"hmdb":[
+"HMDB00148",
+"HMDB60475"
+],
+"inchi_key":[
+"WHUUTDBJXJRKMK-VKHMYHEASA-M"
+],
+"kegg.compound":[
+"C00025",
+"C00302"
+],
+"kegg.drug":[
+"D00007",
+"D04341"
+],
+"metanetx.chemical":[
+"MNXM89557"
+],
+"reactome.compound":[
+"428614",
+"29404",
+"113552",
+"210382"
+],
+"sabiork":[
+"73",
+"2010"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27177",
+"cpd00023",
+"cpd19002"
+]
+}
+},
+{
+"id":"glu__L_e",
+"name":"L-Glutamate",
+"compartment":"e",
+"charge":-1,
+"formula":"C5H8NO4",
+"notes":{
+"original_bigg_ids":[
+"glu_L_e"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glu__L"
+],
+"biocyc":[
+"META:Glutamates",
+"META:GLT"
+],
+"chebi":[
+"CHEBI:76051",
+"CHEBI:21301",
+"CHEBI:29985",
+"CHEBI:42825",
+"CHEBI:29987",
+"CHEBI:18237",
+"CHEBI:24314",
+"CHEBI:16015",
+"CHEBI:13107",
+"CHEBI:5431",
+"CHEBI:21304",
+"CHEBI:6224",
+"CHEBI:14321",
+"CHEBI:29988"
+],
+"hmdb":[
+"HMDB00148",
+"HMDB60475"
+],
+"inchi_key":[
+"WHUUTDBJXJRKMK-VKHMYHEASA-M"
+],
+"kegg.compound":[
+"C00025",
+"C00302"
+],
+"kegg.drug":[
+"D00007",
+"D04341"
+],
+"metanetx.chemical":[
+"MNXM89557"
+],
+"reactome.compound":[
+"428614",
+"29404",
+"113552",
+"210382"
+],
+"sabiork":[
+"73",
+"2010"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd27177",
+"cpd00023",
+"cpd19002"
+]
+}
+},
+{
+"id":"glx_c",
+"name":"Glyoxylate",
+"compartment":"c",
+"charge":-1,
+"formula":"C2H1O3",
+"notes":{
+"original_bigg_ids":[
+"glx_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"glx"
+],
+"biocyc":[
+"META:GLYOX"
+],
+"chebi":[
+"CHEBI:24420",
+"CHEBI:36655",
+"CHEBI:14368",
+"CHEBI:24421",
+"CHEBI:42767",
+"CHEBI:16891",
+"CHEBI:35977",
+"CHEBI:5509"
+],
+"envipath":[
+"32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/cdffdb1a-3322-4cc1-9171-d857bfaa198a",
+"4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/aecbda66-6e98-4c11-aeaf-6a072f4f963c",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/9dc0aa3b-447a-4b5d-8157-501b036f9626",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/43b74f4f-bc8a-4b8b-b587-c97d8e9eed48"
+],
+"hmdb":[
+"HMDB00119"
+],
+"inchi_key":[
+"HHLFWLYXYJOTON-UHFFFAOYSA-M"
+],
+"kegg.compound":[
+"C00048"
+],
+"metanetx.chemical":[
+"MNXM69"
+],
+"reactome.compound":[
+"904849",
+"389678"
+],
+"sabiork":[
+"1838"
+],
+"sbo":"SBO:0000247",
+"seed.compound":[
+"cpd00040"
+]
+}
+},
+{
+"id":"h2o_c",
+"name":"H2O H2O",
+"compartment":"c",
+"charge":0,
+"formula":"H2O",
+"notes":{
+"original_bigg_ids":[
+"h2o_c"
+]
+},
+"annotation":{
+"bigg.metabolite":[
+"h2o"
+],
+"biocyc":[
+"META:CPD-15815",
+"META:OXONIUM",
+"META:HYDROXYL-GROUP",
+"META:WATER",
+"META:OH"
+],
+"chebi":[
+"CHEBI:13352",
+"CHEBI:30490",
+"CHEBI:43228",
+"CHEBI:33813",
+"CHEBI:44292",
+"CHEBI:44641",
+"CHEBI:27313",
+"CHEBI:42043",
+"CHEBI:44819",
+"CHEBI:29356",
+"CHEBI:5594",
+"CHEBI:10743",
+"CHEBI:15377",
+"CHEBI:42857",
+"CHEBI:13365",
+"CHEBI:29412",
+"CHEBI:16234",
+"CHEBI:13419",
+"CHEBI:5585",
+"CHEBI:44701"
+],
+"envipath":[
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/799908db-b8c9-4982-86cb-1f225e2ad08c",
+"650babc9-9d68-4b73-9332-11972ca26f7b/compound/e7f34a8e-cded-4793-b6d5-792335b38636",
+"5882df9c-dae1-4d80-a40e-db4724271456/compound/969d0227-3069-4e44-9525-7ae7bad84170"
+],
+"hmdb":[
+"HMDB02111",
+"HMDB01039"
+],
+"inchi_key":[
+"XLYOFNOQVPJJNP-UHFFFAOYSA-N"
+],
+"kegg.compound":[
+"C00001",
+"C01328"
+],
+"kegg.drug":[
+"D00001",
+"D06322"
+],
+"metanetx.chemical":[
+"MNXM2"
+],
+"reactome.compound":[
+"113521",
+"141343",
+"2022884",
+"5278291",
+"29356",
+"189422",
+"5668574",
+"5693747",
+"109276",
+"113519",
+"1605715",
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+"ecogene":[
+"EG10804"
+],
+"ncbigene":[
+"946179"
+],
+"ncbigi":[
+"16129632"
+],
+"refseq_locus_tag":[
+"b1676"
+],
+"refseq_name":[
+"pykF"
+],
+"refseq_synonym":[
+"ECK1672",
+"JW1666"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AD61"
+]
+}
+},
+{
+"id":"b1854",
+"name":"pykA",
+"notes":{
+"original_bigg_ids":[
+"b1854"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0006182"
+],
+"ecogene":[
+"EG10803"
+],
+"ncbigene":[
+"946527"
+],
+"ncbigi":[
+"16129807"
+],
+"refseq_locus_tag":[
+"b1854"
+],
+"refseq_name":[
+"pykA"
+],
+"refseq_synonym":[
+"JW1843",
+"ECK1855"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P21599"
+]
+}
+},
+{
+"id":"b3386",
+"name":"rpe",
+"notes":{
+"original_bigg_ids":[
+"b3386"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0011061"
+],
+"ecogene":[
+"EG11960"
+],
+"ncbigene":[
+"947896"
+],
+"ncbigi":[
+"16131264"
+],
+"refseq_locus_tag":[
+"b3386"
+],
+"refseq_name":[
+"rpe"
+],
+"refseq_synonym":[
+"yhfD",
+"ECK3373",
+"JW3349",
+"dod"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AG07"
+]
+}
+},
+{
+"id":"b4301",
+"name":"sgcE",
+"notes":{
+"original_bigg_ids":[
+"b4301"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0014097"
+],
+"ecogene":[
+"EG12553"
+],
+"ncbigene":[
+"948829"
+],
+"ncbigi":[
+"16132122"
+],
+"refseq_locus_tag":[
+"b4301"
+],
+"refseq_name":[
+"sgcE"
+],
+"refseq_synonym":[
+"JW4263",
+"ECK4290",
+"yjhK"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P39362"
+]
+}
+},
+{
+"id":"b2914",
+"name":"rpiA",
+"notes":{
+"original_bigg_ids":[
+"b2914"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009567"
+],
+"ecogene":[
+"EG11443"
+],
+"ncbigene":[
+"947407"
+],
+"ncbigi":[
+"16130815"
+],
+"refseq_locus_tag":[
+"b2914"
+],
+"refseq_name":[
+"rpiA"
+],
+"refseq_synonym":[
+"ECK2910",
+"JW5475",
+"ygfC"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A7Z0"
+]
+}
+},
+{
+"id":"b4090",
+"name":"rpiB",
+"notes":{
+"original_bigg_ids":[
+"b4090"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0013405"
+],
+"ecogene":[
+"EG11827"
+],
+"ncbigene":[
+"948602"
+],
+"ncbigi":[
+"16131916"
+],
+"refseq_locus_tag":[
+"b4090"
+],
+"refseq_name":[
+"rpiB"
+],
+"refseq_synonym":[
+"JW4051",
+"alsB",
+"alsI",
+"yjcA",
+"ECK4083"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P37351"
+]
+}
+},
+{
+"id":"b0721",
+"name":"sdhC",
+"notes":{
+"original_bigg_ids":[
+"b0721"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002460"
+],
+"ecogene":[
+"EG10933"
+],
+"ncbigene":[
+"945316"
+],
+"ncbigi":[
+"16128696"
+],
+"refseq_locus_tag":[
+"b0721"
+],
+"refseq_name":[
+"sdhC"
+],
+"refseq_synonym":[
+"JW0711",
+"ECK0710",
+"cybA"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P69054"
+]
+}
+},
+{
+"id":"b0722",
+"name":"sdhD",
+"notes":{
+"original_bigg_ids":[
+"b0722"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002464"
+],
+"ecogene":[
+"EG10934"
+],
+"ncbigene":[
+"945322"
+],
+"ncbigi":[
+"16128697"
+],
+"refseq_locus_tag":[
+"b0722"
+],
+"refseq_name":[
+"sdhD"
+],
+"refseq_synonym":[
+"JW0712",
+"ECK0711"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC44"
+]
+}
+},
+{
+"id":"b0724",
+"name":"sdhB",
+"notes":{
+"original_bigg_ids":[
+"b0724"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002468"
+],
+"ecogene":[
+"EG10932"
+],
+"ncbigene":[
+"945300"
+],
+"ncbigi":[
+"16128699"
+],
+"refseq_locus_tag":[
+"b0724"
+],
+"refseq_name":[
+"sdhB"
+],
+"refseq_synonym":[
+"ECK0713",
+"JW0714"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P07014"
+]
+}
+},
+{
+"id":"b0723",
+"name":"sdhA",
+"notes":{
+"original_bigg_ids":[
+"b0723"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002466"
+],
+"ecogene":[
+"EG10931"
+],
+"ncbigene":[
+"945402"
+],
+"ncbigi":[
+"16128698"
+],
+"refseq_locus_tag":[
+"b0723"
+],
+"refseq_name":[
+"sdhA"
+],
+"refseq_synonym":[
+"JW0713",
+"ECK0712"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AC41"
+]
+}
+},
+{
+"id":"b0729",
+"name":"sucD",
+"notes":{
+"original_bigg_ids":[
+"b0729"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002485"
+],
+"ecogene":[
+"EG10982"
+],
+"ncbigene":[
+"945314"
+],
+"ncbigi":[
+"16128704"
+],
+"refseq_locus_tag":[
+"b0729"
+],
+"refseq_name":[
+"sucD"
+],
+"refseq_synonym":[
+"JW0718",
+"ECK0717"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0AGE9"
+]
+}
+},
+{
+"id":"b0728",
+"name":"sucC",
+"notes":{
+"original_bigg_ids":[
+"b0728"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0002483"
+],
+"ecogene":[
+"EG10981"
+],
+"ncbigene":[
+"945312"
+],
+"ncbigi":[
+"16128703"
+],
+"refseq_locus_tag":[
+"b0728"
+],
+"refseq_name":[
+"sucC"
+],
+"refseq_synonym":[
+"JW0717",
+"ECK0716"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A836"
+]
+}
+},
+{
+"id":"b0008",
+"name":"talB",
+"notes":{
+"original_bigg_ids":[
+"b0008"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0000027"
+],
+"ecogene":[
+"EG11556"
+],
+"ncbigene":[
+"944748"
+],
+"ncbigi":[
+"16128002"
+],
+"refseq_locus_tag":[
+"b0008"
+],
+"refseq_name":[
+"talB"
+],
+"refseq_synonym":[
+"yaaK",
+"JW0007",
+"ECK0008"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A870"
+]
+}
+},
+{
+"id":"b2464",
+"name":"talA",
+"notes":{
+"original_bigg_ids":[
+"b2464"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008115"
+],
+"ecogene":[
+"EG11797"
+],
+"ncbigene":[
+"947006"
+],
+"ncbigi":[
+"16130389"
+],
+"refseq_locus_tag":[
+"b2464"
+],
+"refseq_name":[
+"talA"
+],
+"refseq_synonym":[
+"ECK2459",
+"JW2448"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A867"
+]
+}
+},
+{
+"id":"b2465",
+"name":"tktB",
+"notes":{
+"original_bigg_ids":[
+"b2465"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0008117"
+],
+"ecogene":[
+"EG12100"
+],
+"ncbigene":[
+"945865"
+],
+"ncbigi":[
+"16130390"
+],
+"refseq_locus_tag":[
+"b2465"
+],
+"refseq_name":[
+"tktB"
+],
+"refseq_synonym":[
+"JW2449",
+"ECK2460"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P33570"
+]
+}
+},
+{
+"id":"b2935",
+"name":"tktA",
+"notes":{
+"original_bigg_ids":[
+"b2935"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0009625"
+],
+"ecogene":[
+"EG11427"
+],
+"ncbigene":[
+"947420"
+],
+"ncbigi":[
+"49176286"
+],
+"refseq_locus_tag":[
+"b2935"
+],
+"refseq_name":[
+"tktA"
+],
+"refseq_synonym":[
+"JW5478",
+"tkt",
+"ECK2930"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P27302"
+]
+}
+},
+{
+"id":"b3919",
+"name":"tpiA",
+"notes":{
+"original_bigg_ids":[
+"b3919"
+]
+},
+"annotation":{
+"asap":[
+"ABE-0012799"
+],
+"ecogene":[
+"EG11015"
+],
+"ncbigene":[
+"948409"
+],
+"ncbigi":[
+"16131757"
+],
+"refseq_locus_tag":[
+"b3919"
+],
+"refseq_name":[
+"tpiA"
+],
+"refseq_synonym":[
+"JW3890",
+"ECK3911",
+"tpi"
+],
+"sbo":"SBO:0000243",
+"uniprot":[
+"P0A858"
+]
+}
+}
+],
+"id":"e_coli_core",
+"compartments":{
+"c":"cytosol",
+"e":"extracellular space"
+},
+"version":"1"
+}
\ No newline at end of file
diff --git a/tests/data/e_coli_core_for_annotation.xml b/tests/data/e_coli_core_for_annotation.xml
new file mode 100644
index 000000000..5658f8fdb
--- /dev/null
+++ b/tests/data/e_coli_core_for_annotation.xml
@@ -0,0 +1,8367 @@
+
+
+
+
+
+
+
Key1 : Value1
+
+
+
e_coli_core - Escherichia coli str. K-12 substr. MG1655
+
+
+
Description
+
+
This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in
+ SBML format.
+
The content of this model has been carefully created in a manual research effort. This file has been exported from the software
+
COBRApy and further processed with the
+
JSBML-based
+
ModelPolisher application.
Terms of use
+ Copyright © 2017 The Regents of the University of California.
+
+
Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met:
+
+ - Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
+ - Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided
+ with the distribution.
+
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
For specific licensing terms about this particular model and regulations of commercial use, see
+ this model in BiGG Models knowledge-base.
+
References
When using content from BiGG Models knowledge-base in your research works, please cite
+
+ - King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015).
+
- BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models.
+ Nucl Acids Res.
+ doi:10.1093/nar/gkv1049
+
+
+
+
+
+
+
+
+
+ Koenig
+ Matthias
+
+ koenigmx@hu-berlin.de
+
+ Humboldt-University Berlin, Institute for Theoretical Biology
+
+
+
+
+ Koenig
+ Matthias
+
+ koenigmx@hu-berlin.de
+
+
+
+ Koenig
+ Matthias
+
+
+ Humboldt-University Berlin, Institute for Theoretical Biology
+
+
+
+
+ Koenig
+ Matthias
+
+
+
+
+
+ 2019-03-06T14:40:55Z
+
+
+ 2019-03-06T14:40:55Z
+
+
+ 2019-03-06T14:41:55Z
+
+
+
+
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Key1 : Value1
+
Key2 : Value2
+
+
A Heading
+
e_coli_core - Escherichia coli str. K-12 substr. MG1655
+
+
Key3 : Value3
+
Description
\n \n
This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in\n SBML\u00a0format.
\n
The content of this model has been carefully created in a manual research effort. This file has been exported from the software\n
COBRApy\u00a0and further processed with the\n
JSBML-based\n
ModelPolisher\u00a0application.
Terms of use
\n Copyright \u00a9 2017 The Regents of the University of California.
\n \n
Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met:\n
\n - Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
\n - Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided\n with the distribution.
\n
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n
For specific licensing terms about this particular model and regulations of commercial use, see\n this model in BiGG Models knowledge-base.
\n
References
When using content from BiGG Models knowledge-base in your research works, please cite\n \n - King ZA, Lu JS, Dr\u00e4ger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and\u00a0Lewis NE. (2015).\n
- BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models.\n Nucl Acids Res.\n doi:10.1093/nar/gkv1049
\n
\n ",
+ "reactions": [
+ {
+ "annotation": {
+ "cvterms": {
+ "bqb_is": [
+ {
+ "resources": [
+ "http://identifiers.org/bigg.reaction/ACALD",
+ "http://identifiers.org/biocyc/META:ACETALD-DEHYDROG-RXN",
+ "http://identifiers.org/ec-code/1.2.1.10",
+ "http://identifiers.org/kegg.reaction/R00228",
+ "http://identifiers.org/metanetx.reaction/MNXR95210",
+ "http://identifiers.org/rhea/23288",
+ "http://identifiers.org/rhea/23289",
+ "http://identifiers.org/rhea/23290",
+ "http://identifiers.org/rhea/23291"
+ ]
+ }
+ ]
+ }
+ },
+ "gene_reaction_rule": "b0351 or b1241",
+ "id": "R_ACALD",
+ "lower_bound": -1000.0,
+ "metabolites": {
+ "M_acald_c": -1.0,
+ "M_accoa_c": 1.0,
+ "M_coa_c": -1.0,
+ "M_h_c": 1.0,
+ "M_nad_c": -1.0,
+ "M_nadh_c": 1.0
+ },
+ "name": "Acetaldehyde dehydrogenase (acetylating)",
+ "notes": "\n \n \n
Key1 : Value1
\n
Key2 : Value2
\n
\n
A Heading
\n
e_coli_core - Escherichia coli str. K-12 substr. MG1655
\n
\n
Key3 : Value3
\n
\n
Key1 : Value1
\n
\n
\n
e_coli_core - Escherichia coli str. K-12 substr. MG1655
\n \n
\n