Constants

Constants for PyBEL.

This module maintains the strings used throughout the PyBEL codebase to promote consistency.

pybel.constants.get_cache_connection()

Get the preferred RFC-1738 database connection string.

1. Check the environment variable PYBEL_CONNECTION

2. Check the PYBEL_CONNECTION key in the config file ~/.config/pybel/config.json. Optionally, this config file might be in a different place if the environment variable PYBEL_CONFIG_DIRECTORY has been set.

3. Return a default connection string using a SQLite database in the ~/.pybel. Optionally, this directory might be in a different place if the environment variable PYBEL_RESOURCE_DIRECTORY has been set.

Return type

str

pybel.constants.NAMESPACE_DOMAIN_TYPES = {'BiologicalProcess', 'Chemical', 'Gene and Gene Products', 'Other'}

The valid namespace types .. seealso:: https://wiki.openbel.org/display/BELNA/Custom+Namespaces

pybel.constants.CITATION_DATE = 'date'

Represents the key for the citation date in a citation dictionary

pybel.constants.CITATION_AUTHORS = 'authors'

Represents the key for the citation authors in a citation dictionary

pybel.constants.CITATION_JOURNAL = 'journal'

Represents the key for the citation comment in a citation dictionary

pybel.constants.CITATION_VOLUME = 'volume'

Represents the key for the optional PyBEL citation volume entry in a citation dictionary

pybel.constants.CITATION_ISSUE = 'issue'

Represents the key for the optional PyBEL citation issue entry in a citation dictionary

pybel.constants.CITATION_PAGES = 'pages'

Represents the key for the optional PyBEL citation pages entry in a citation dictionary

pybel.constants.CITATION_FIRST_AUTHOR = 'first'

Represents the key for the optional PyBEL citation first author entry in a citation dictionary

pybel.constants.CITATION_LAST_AUTHOR = 'last'

Represents the key for the optional PyBEL citation last author entry in a citation dictionary

pybel.constants.CITATION_ARTICLE_TYPE = 'article_type'

Represents the type of article (Journal Article, Review, etc.)

pybel.constants.FUNCTION = 'function'

The node data key specifying the node’s function (e.g. GENE, MIRNA, BIOPROCESS, etc.)

pybel.constants.CONCEPT = 'concept'

The key specifying a concept

pybel.constants.NAMESPACE = 'namespace'

The key specifying an identifier dictionary’s namespace. Used for nodes, activities, and transformations.

pybel.constants.NAME = 'name'

The key specifying an identifier dictionary’s name. Used for nodes, activities, and transformations.

pybel.constants.IDENTIFIER = 'identifier'

The key specifying an identifier dictionary

pybel.constants.LABEL = 'label'

The key specifying an optional label for the node

pybel.constants.DESCRIPTION = 'description'

The key specifying an optional description for the node

pybel.constants.XREFS = 'xref'

The key specifying xrefs

pybel.constants.MEMBERS = 'members'

They key representing the nodes that are a member of a composite or complex

pybel.constants.REACTANTS = 'reactants'

The key representing the nodes appearing in the reactant side of a biochemical reaction

pybel.constants.PRODUCTS = 'products'

The key representing the nodes appearing in the product side of a biochemical reaction

pybel.constants.PARTNER_3P = 'partner_3p'

The key specifying the identifier dictionary of the fusion’s 3-Prime partner

pybel.constants.PARTNER_5P = 'partner_5p'

The key specifying the identifier dictionary of the fusion’s 5-Prime partner

pybel.constants.RANGE_3P = 'range_3p'

The key specifying the range dictionary of the fusion’s 3-Prime partner

pybel.constants.RANGE_5P = 'range_5p'

The key specifying the range dictionary of the fusion’s 5-Prime partner

pybel.constants.VARIANTS = 'variants'

The key specifying the node has a list of associated variants

pybel.constants.KIND = 'kind'

The key representing what kind of variation is being represented

pybel.constants.HGVS = 'hgvs'

The value for KIND for an HGVS variant

pybel.constants.PMOD = 'pmod'

The value for KIND for a protein modification

pybel.constants.GMOD = 'gmod'

The value for KIND for a gene modification

pybel.constants.FRAGMENT = 'frag'

The value for KIND for a fragment

pybel.constants.PYBEL_VARIANT_KINDS = {'frag', 'gmod', 'hgvs', 'pmod'}

The allowed values for KIND

pybel.constants.PYBEL_NODE_DATA_KEYS = {'function', 'fusion', 'identifier', 'members', 'name', 'namespace', 'products', 'reactants', 'variants'}

The group of all BEL-provided keys for node data dictionaries, used for hashing.

pybel.constants.DIRTY = 'dirty'

Used as a namespace when none is given when lenient parsing mode is turned on. Not recommended!

pybel.constants.ABUNDANCE = 'Abundance'

Represents the BEL abundance, abundance()

pybel.constants.GENE = 'Gene'

Represents the BEL abundance, geneAbundance() .. seealso:: http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#Xabundancea

pybel.constants.RNA = 'RNA'

Represents the BEL abundance, rnaAbundance()

pybel.constants.MIRNA = 'miRNA'

Represents the BEL abundance, microRNAAbundance()

pybel.constants.PROTEIN = 'Protein'

Represents the BEL abundance, proteinAbundance()

pybel.constants.BIOPROCESS = 'BiologicalProcess'

Represents the BEL function, biologicalProcess()

pybel.constants.PATHOLOGY = 'Pathology'

Represents the BEL function, pathology()

pybel.constants.POPULATION = 'Population'

Represents the BEL function, populationAbundance()

pybel.constants.COMPOSITE = 'Composite'

Represents the BEL abundance, compositeAbundance()

pybel.constants.COMPLEX = 'Complex'

Represents the BEL abundance, complexAbundance()

pybel.constants.REACTION = 'Reaction'

Represents the BEL transformation, reaction()

pybel.constants.PYBEL_NODE_FUNCTIONS = {'Abundance', 'BiologicalProcess', 'Complex', 'Composite', 'Gene', 'Pathology', 'Population', 'Protein', 'RNA', 'Reaction', 'miRNA'}

A set of all of the valid PyBEL node functions

pybel.constants.rev_abundance_labels = {'Abundance': 'a', 'BiologicalProcess': 'bp', 'Complex': 'complex', 'Composite': 'composite', 'Gene': 'g', 'Pathology': 'path', 'Population': 'pop', 'Protein': 'p', 'RNA': 'r', 'miRNA': 'm'}

The mapping from PyBEL node functions to BEL strings

pybel.constants.RELATION = 'relation'

The key for an internal edge data dictionary for the relation string

pybel.constants.CITATION = 'citation'

The key for an internal edge data dictionary for the citation dictionary

pybel.constants.EVIDENCE = 'evidence'

The key for an internal edge data dictionary for the evidence string

pybel.constants.ANNOTATIONS = 'annotations'

The key for an internal edge data dictionary for the annotations dictionary

pybel.constants.SOURCE_MODIFIER = 'source_modifier'

The key for an internal edge data dictionary for the source modifier dictionary

pybel.constants.TARGET_MODIFIER = 'target_modifier'

The key for an internal edge data dictionary for the target modifier dictionary

pybel.constants.LINE = 'line'

The key or an internal edge data dictionary for the line number

pybel.constants.HASH = 'hash'

The key representing the hash of the other

pybel.constants.PYBEL_EDGE_DATA_KEYS = {'annotations', 'citation', 'evidence', 'relation', 'source_modifier', 'target_modifier'}

The group of all BEL-provided keys for edge data dictionaries, used for hashing.

pybel.constants.PYBEL_EDGE_METADATA_KEYS = {'hash', 'line'}

The group of all PyBEL-specific keys for edge data dictionaries, not used for hashing.

pybel.constants.PYBEL_EDGE_ALL_KEYS = {'annotations', 'citation', 'evidence', 'hash', 'line', 'relation', 'source_modifier', 'target_modifier'}

The group of all PyBEL annotated keys for edge data dictionaries

pybel.constants.HAS_REACTANT = 'hasReactant'

A BEL relationship

pybel.constants.HAS_PRODUCT = 'hasProduct'

A BEL relationship

pybel.constants.HAS_VARIANT = 'hasVariant'

A BEL relationship

pybel.constants.TRANSCRIBED_TO = 'transcribedTo'

A BEL relationship GENE to RNA is called transcription

pybel.constants.TRANSLATED_TO = 'translatedTo'

A BEL relationship RNA to PROTEIN is called translation

pybel.constants.INCREASES = 'increases'

A BEL relationship

pybel.constants.DIRECTLY_INCREASES = 'directlyIncreases'

A BEL relationship

pybel.constants.DECREASES = 'decreases'

A BEL relationship

pybel.constants.DIRECTLY_DECREASES = 'directlyDecreases'

A BEL relationship

pybel.constants.CAUSES_NO_CHANGE = 'causesNoChange'

A BEL relationship

pybel.constants.REGULATES = 'regulates'

A BEL relationship

pybel.constants.BINDS = 'binds'

A BEL relationship

pybel.constants.CORRELATION = 'correlation'

A BEL relationship

pybel.constants.NO_CORRELATION = 'noCorrelation'

A BEL relationship

pybel.constants.NEGATIVE_CORRELATION = 'negativeCorrelation'

A BEL relationship

pybel.constants.POSITIVE_CORRELATION = 'positiveCorrelation'

A BEL relationship

pybel.constants.ASSOCIATION = 'association'

A BEL relationship

pybel.constants.ORTHOLOGOUS = 'orthologous'

A BEL relationship

pybel.constants.ANALOGOUS_TO = 'analogousTo'

A BEL relationship

pybel.constants.IS_A = 'isA'

A BEL relationship

pybel.constants.RATE_LIMITING_STEP_OF = 'rateLimitingStepOf'

A BEL relationship

pybel.constants.SUBPROCESS_OF = 'subProcessOf'

A BEL relationship

pybel.constants.BIOMARKER_FOR = 'biomarkerFor'

A BEL relationship

pybel.constants.PROGONSTIC_BIOMARKER_FOR = 'prognosticBiomarkerFor'

A BEL relationship

pybel.constants.EQUIVALENT_TO = 'equivalentTo'

A BEL relationship, added by PyBEL

pybel.constants.PART_OF = 'partOf'

A BEL relationship, added by PyBEL

pybel.constants.CAUSAL_INCREASE_RELATIONS = {'directlyIncreases', 'increases'}

A set of all causal relationships that have an increasing effect

pybel.constants.CAUSAL_DECREASE_RELATIONS = {'decreases', 'directlyDecreases'}

A set of all causal relationships that have a decreasing effect

pybel.constants.DIRECT_CAUSAL_RELATIONS = {'directlyDecreases', 'directlyIncreases'}

A set of direct causal relations

pybel.constants.INDIRECT_CAUSAL_RELATIONS = {'decreases', 'increases', 'regulates'}

A set of direct causal relations

pybel.constants.CAUSAL_POLAR_RELATIONS = {'decreases', 'directlyDecreases', 'directlyIncreases', 'increases'}

A set of causal relationships that are polar

pybel.constants.CAUSAL_RELATIONS = {'decreases', 'directlyDecreases', 'directlyIncreases', 'increases', 'regulates'}

A set of all causal relationships

pybel.constants.CORRELATIVE_RELATIONS = {'correlation', 'negativeCorrelation', 'noCorrelation', 'positiveCorrelation'}

A set of all correlative relationships

pybel.constants.POLAR_RELATIONS = {'decreases', 'directlyDecreases', 'directlyIncreases', 'increases', 'negativeCorrelation', 'positiveCorrelation'}

A set of polar relations

pybel.constants.TWO_WAY_RELATIONS = {'analogousTo', 'association', 'binds', 'correlation', 'equivalentTo', 'negativeCorrelation', 'noCorrelation', 'orthologous', 'positiveCorrelation'}

A set of all relationships that are inherently directionless, and are therefore added to the graph twice

pybel.constants.UNQUALIFIED_EDGES = {'equivalentTo', 'hasProduct', 'hasReactant', 'hasVariant', 'isA', 'orthologous', 'partOf', 'transcribedTo', 'translatedTo'}

A list of relationship types that don’t require annotations or evidence

pybel.constants.GRAPH_METADATA = 'document_metadata'

The key for the document metadata dictionary. Can be accessed by graph.graph[GRAPH_METADATA], or by using the property built in to the pybel.BELGraph, pybel.BELGraph.document()

pybel.constants.METADATA_NAME = 'name'

The key for the document name. Can be accessed by graph.document[METADATA_NAME] or by using the property built into the pybel.BELGraph class, pybel.BELGraph.name()

pybel.constants.METADATA_VERSION = 'version'

The key for the document version. Can be accessed by graph.document[METADATA_VERSION]

pybel.constants.METADATA_DESCRIPTION = 'description'

The key for the document description. Can be accessed by graph.document[METADATA_DESCRIPTION]

pybel.constants.METADATA_AUTHORS = 'authors'

The key for the document authors. Can be accessed by graph.document[METADATA_NAME]

pybel.constants.METADATA_CONTACT = 'contact'

The key for the document contact email. Can be accessed by graph.document[METADATA_CONTACT]

pybel.constants.METADATA_LICENSES = 'licenses'

The key for the document licenses. Can be accessed by graph.document[METADATA_LICENSES]

pybel.constants.METADATA_COPYRIGHT = 'copyright'

The key for the document copyright information. Can be accessed by graph.document[METADATA_COPYRIGHT]

pybel.constants.METADATA_DISCLAIMER = 'disclaimer'

The key for the document disclaimer. Can be accessed by graph.document[METADATA_DISCLAIMER]

pybel.constants.METADATA_PROJECT = 'project'

The key for the document project. Can be accessed by graph.document[METADATA_PROJECT]

pybel.constants.DOCUMENT_KEYS = {'Authors': 'authors', 'ContactInfo': 'contact', 'Copyright': 'copyright', 'Description': 'description', 'Disclaimer': 'disclaimer', 'Licenses': 'licenses', 'Name': 'name', 'Project': 'project', 'Version': 'version'}

Provides a mapping from BEL language keywords to internal PyBEL strings

pybel.constants.METADATA_INSERT_KEYS = {'authors', 'contact', 'copyright', 'description', 'disclaimer', 'licenses', 'name', 'version'}

The keys to use when inserting a graph to the cache

pybel.constants.INVERSE_DOCUMENT_KEYS = {'authors': 'Authors', 'contact': 'ContactInfo', 'copyright': 'Copyright', 'description': 'Description', 'disclaimer': 'Disclaimer', 'licenses': 'Licenses', 'name': 'Name', 'project': 'Project', 'version': 'Version'}

Provides a mapping from internal PyBEL strings to BEL language keywords. Is the inverse of DOCUMENT_KEYS

pybel.constants.REQUIRED_METADATA = {'authors', 'contact', 'description', 'name', 'version'}

A set representing the required metadata during BEL document parsing

pybel.constants.FRAGMENT_START = 'start'

The key for the starting position of a fragment range

pybel.constants.FRAGMENT_STOP = 'stop'

The key for the stopping position of a fragment range

pybel.constants.FRAGMENT_MISSING = 'missing'

The key signifying that there is neither a start nor stop position defined

pybel.constants.FRAGMENT_DESCRIPTION = 'description'

The key for any additional descriptive data about a fragment

pybel.constants.GMOD_ORDER = ['kind', 'identifier']

The order for serializing gene modification data

pybel.constants.GSUB_REFERENCE = 'reference'

The key for the reference nucleotide in a gene substitution. Only used during parsing since this is converted to HGVS.

pybel.constants.GSUB_POSITION = 'position'

The key for the position of a gene substitution. Only used during parsing since this is converted to HGVS

pybel.constants.GSUB_VARIANT = 'variant'

The key for the effect of a gene substitution. Only used during parsing since this is converted to HGVS

pybel.constants.PMOD_CODE = 'code'

The key for the protein modification code.

pybel.constants.PMOD_POSITION = 'pos'

The key for the protein modification position.

pybel.constants.PMOD_ORDER = ['kind', 'identifier', 'code', 'pos']

The order for serializing information about a protein modification

pybel.constants.PSUB_REFERENCE = 'reference'

The key for the reference amino acid in a protein substitution. Only used during parsing since this is concerted to HGVS

pybel.constants.PSUB_POSITION = 'position'

The key for the position of a protein substitution. Only used during parsing since this is converted to HGVS.

pybel.constants.PSUB_VARIANT = 'variant'

The key for the variant of a protein substitution.Only used during parsing since this is converted to HGVS.

pybel.constants.TRUNCATION_POSITION = 'position'

The key for the position at which a protein is truncated

pybel.constants.belns_encodings = {'A': {'Abundance', 'Complex', 'Gene', 'Protein', 'RNA', 'miRNA'}, 'B': {'BiologicalProcess', 'Pathology'}, 'C': {'Complex'}, 'G': {'Gene'}, 'M': {'miRNA'}, 'O': {'Pathology'}, 'P': {'Protein'}, 'R': {'RNA', 'miRNA'}}

The mapping from BEL namespace codes to PyBEL internal abundance constants ..seealso:: https://wiki.openbel.org/display/BELNA/Assignment+of+Encoding+%28Allowed+Functions%29+for+BEL+Namespaces

Language constants for BEL.

This module contains mappings between PyBEL’s internal constants and BEL language keywords.

class pybel.language.Entity(*, namespace, name=None, identifier=None)

Represents a named entity with a namespace and name/identifier.

Create a dictionary representing a reference to an entity.

Parameters

• namespace (str) – The namespace to which the entity belongs

• name (Optional[str]) – The name of the entity

• identifier (Optional[str]) – The identifier of the entity in the namespace

property namespace

The entity’s namespace.

Return type

str

property name

The entity’s name or label.

Return type

str

property identifier

The entity’s identifier.

Return type

str

property curie

Return this entity as a CURIE.

Return type

str

property obo

Return this entity as an OBO-style CURIE.

Return type

str

pybel.language.activity_labels = {'cat': 'cat', 'catalyticActivity': 'cat', 'chap': 'chap', 'chaperoneActivity': 'chap', 'gap': 'gap', 'gef': 'gef', 'gtp': 'gtp', 'gtpBoundActivity': 'gtp', 'gtpaseActivatingProteinActivity': 'gap', 'guanineNucleotideExchangeFactorActivity': 'gef', 'kin': 'kin', 'kinaseActivity': 'kin', 'molecularActivity': 'molecularActivity', 'pep': 'pep', 'peptidaseActivity': 'pep', 'phos': 'phos', 'phosphataseActivity': 'phos', 'ribo': 'ribo', 'ribosylationActivity': 'ribo', 'tport': 'tport', 'transcriptionalActivity': 'tscript', 'transportActivity': 'tport', 'tscript': 'tscript'}

A dictionary of activity labels used in the ma() function in activity(p(X), ma(Y))

pybel.language.activity_mapping = {'act': {'identifier': '0003674', 'name': 'molecular function', 'namespace': 'go'}, 'cat': {'identifier': '0003824', 'name': 'catalytic activity', 'namespace': 'go'}, 'chap': {'identifier': '0044183', 'name': 'protein binding involved in protein folding', 'namespace': 'go'}, 'gap': {'identifier': '0032794', 'name': 'GTPase activating protein binding', 'namespace': 'go'}, 'gef': {'identifier': '0005085', 'name': 'guanyl-nucleotide exchange factor activity', 'namespace': 'go'}, 'gtp': {'identifier': '0005525', 'name': 'GTP binding', 'namespace': 'go'}, 'kin': {'identifier': '0016301', 'name': 'kinase activity', 'namespace': 'go'}, 'molecularActivity': {'identifier': '0003674', 'name': 'molecular_function', 'namespace': 'go'}, 'pep': {'identifier': '0008233', 'name': 'peptidase activity', 'namespace': 'go'}, 'phos': {'identifier': '0016791', 'name': 'phosphatase activity', 'namespace': 'go'}, 'ribo': {'identifier': '0003956', 'name': 'NAD(P)+-protein-arginine ADP-ribosyltransferase activity', 'namespace': 'go'}, 'tport': {'identifier': '0005215', 'name': 'transporter activity', 'namespace': 'go'}, 'tscript': {'identifier': '0001071', 'name': 'nucleic acid binding transcription factor activity', 'namespace': 'go'}}

Maps the default BEL molecular activities to Gene Ontology Molecular Functions

pybel.language.compartment_mapping = {'cell surface': {'identifier': '0009986', 'name': 'cell surface', 'namespace': 'go'}, 'cytoplasm': {'identifier': '0005737', 'name': 'cytoplasm', 'namespace': 'go'}, 'extracellular space': {'identifier': '0005615', 'name': 'extracellular space', 'namespace': 'go'}, 'intracellular': {'identifier': '0005622', 'name': 'intracellular', 'namespace': 'go'}, 'nucleus': {'identifier': '0005634', 'name': 'nucleus', 'namespace': 'go'}}

Maps the default BEL cellular components to Gene Ontology Cellular Components

pybel.language.abundance_labels = {'a': 'Abundance', 'abundance': 'Abundance', 'biologicalProcess': 'BiologicalProcess', 'bp': 'BiologicalProcess', 'complex': 'Complex', 'complexAbundance': 'Complex', 'composite': 'Composite', 'compositeAbundance': 'Composite', 'g': 'Gene', 'geneAbundance': 'Gene', 'm': 'miRNA', 'microRNAAbundance': 'miRNA', 'p': 'Protein', 'path': 'Pathology', 'pathology': 'Pathology', 'proteinAbundance': 'Protein', 'r': 'RNA', 'rnaAbundance': 'RNA'}

Provides a mapping from BEL terms to PyBEL internal constants

pybel.language.abundance_sbo_mapping = {'BiologicalProcess': {'identifier': '0000375', 'name': 'process', 'namespace': 'sbo'}, 'Complex': {'identifier': '0000297', 'name': 'protein complex', 'namespace': 'sbo'}, 'Gene': {'identifier': '0000243', 'name': 'gene', 'namespace': 'sbo'}, 'Pathology': {'identifier': '0000358', 'name': 'phenotype', 'namespace': 'sbo'}, 'RNA': {'identifier': '0000278', 'name': 'messenger RNA', 'namespace': 'sbo'}, 'miRNA': {'identifier': '0000316', 'name': 'microRNA', 'namespace': 'sbo'}}

Maps the BEL abundance types to the Systems Biology Ontology

pybel.language.pmod_namespace = {'ADP-ribosylation': 'ADPRib', 'ADPRib': 'ADPRib', 'Ac': 'Ac', 'Farn': 'Farn', 'Gerger': 'Gerger', 'Glyco': 'Glyco', 'Hy': 'Hy', 'ISG': 'ISG', 'ISG15-protein conjugation': 'ISG', 'ISGylation': 'ISG', 'Lysine 48-linked polyubiquitination': 'UbK48', 'Lysine 63-linked polyubiquitination': 'UbK63', 'Me': 'Me', 'Me1': 'Me1', 'Me2': 'Me2', 'Me3': 'Me3', 'Myr': 'Myr', 'N-linked glycosylation': 'NGlyco', 'NGlyco': 'NGlyco', 'NO': 'NO', 'Nedd': 'Nedd', 'Nitrosylation': 'NO', 'O-linked glycosylation': 'OGlyco', 'OGlyco': 'OGlyco', 'Ox': 'Ox', 'Palm': 'Palm', 'Ph': 'Ph', 'SUMOylation': 'Sumo', 'Sulf': 'Sulf', 'Sumo': 'Sumo', 'Ub': 'Ub', 'UbK48': 'UbK48', 'UbK63': 'UbK63', 'UbMono': 'UbMono', 'UbPoly': 'UbPoly', 'acetylation': 'Ac', 'adenosine diphosphoribosyl': 'ADPRib', 'di-methylation': 'Me2', 'dimethylation': 'Me2', 'farnesylation': 'Farn', 'geranylgeranylation': 'Gerger', 'glycosylation': 'Glyco', 'hydroxylation': 'Hy', 'methylation': 'Me', 'mono-methylation': 'Me1', 'monomethylation': 'Me1', 'monoubiquitination': 'UbMono', 'myristoylation': 'Myr', 'neddylation': 'Nedd', 'oxidation': 'Ox', 'palmitoylation': 'Palm', 'phosphorylation': 'Ph', 'polyubiquitination': 'UbPoly', 'sulfation': 'Sulf', 'sulfonation': 'sulfonation', 'sulfur addition': 'Sulf', 'sulphation': 'Sulf', 'sulphonation': 'sulfonation', 'sulphur addition': 'Sulf', 'tri-methylation': 'Me3', 'trimethylation': 'Me3', 'ubiquitination': 'Ub', 'ubiquitinylation': 'Ub', 'ubiquitylation': 'Ub'}

A dictionary of default protein modifications to their preferred value

pybel.language.pmod_mappings = {'ADPRib': {'synonyms': ['ADPRib', 'ADP-ribosylation', 'ADPRib', 'ADP-rybosylation', 'adenosine diphosphoribosyl'], 'xrefs': [{'namespace': 'go', 'name': 'protein ADP-ribosylation', 'identifier': '0006471'}, {'namespace': 'mod', 'name': 'adenosine diphosphoribosyl (ADP-ribosyl) modified residue', 'identifier': '00752'}, {'namespace': 'mop', 'name': 'adenosinediphosphoribosylation', 'identifier': '0000220'}]}, 'Ac': {'synonyms': ['Ac', 'acetylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein acetylation', 'identifier': '0006473'}, {'namespace': 'mod', 'name': 'acetylated residue', 'identifier': '00394'}, {'namespace': 'mop', 'name': 'acetylation', 'identifier': '0000030'}, {'namespace': 'sbo', 'name': 'acetylation', 'identifier': '0000215'}]}, 'Farn': {'synonyms': ['Farn', 'farnesylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein farnesylation', 'identifier': '0018343'}, {'namespace': 'mod', 'name': 'farnesylated residue', 'identifier': '00437'}, {'namespace': 'mop', 'name': 'farnesylation', 'identifier': '0000429'}]}, 'Gerger': {'synonyms': ['Gerger', 'geranylgeranylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein geranylgeranylation', 'identifier': '0018344'}, {'namespace': 'mod', 'name': 'geranylgeranylated residue ', 'identifier': '00441'}, {'namespace': 'mop', 'name': 'geranylgeranylation', 'identifier': '0000431'}]}, 'Glyco': {'synonyms': ['Glyco', 'glycosylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein glycosylation', 'identifier': '0006486'}, {'namespace': 'mod', 'name': 'glycosylated residue', 'identifier': '00693'}, {'namespace': 'mop', 'name': 'glycosylation', 'identifier': '0000162'}]}, 'Hy': {'synonyms': ['Hyhydroxylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein hydroxylation', 'identifier': '0018126'}, {'namespace': 'mod', 'name': 'hydroxylated residue', 'identifier': '00677'}, {'namespace': 'mop', 'name': 'hydroxylation', 'identifier': '0000673'}]}, 'ISG': {'activities': [{'namespace': 'go', 'name': 'ISG15 transferase activity', 'identifier': '0042296'}], 'synonyms': ['ISG', 'ISGylation', 'ISG15-protein conjugation'], 'xrefs': [{'namespace': 'go', 'name': 'ISG15-protein conjugation', 'identifier': '0032020'}]}, 'Me': {'synonyms': ['Me', 'methylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein methylation', 'identifier': '0006479'}, {'namespace': 'mod', 'name': 'methylated residue', 'identifier': '00427'}]}, 'Me1': {'is_a': ['Me'], 'synonyms': ['Me1', 'monomethylation', 'mono-methylation'], 'xrefs': [{'namespace': 'mod', 'name': 'monomethylated residue', 'identifier': '00599'}]}, 'Me2': {'is_a': ['Me'], 'synonyms': ['Me2', 'dimethylation', 'di-methylation'], 'xrefs': [{'namespace': 'mod', 'name': 'dimethylated residue', 'identifier': '00429'}]}, 'Me3': {'is_a': ['Me'], 'synonyms': ['Me3', 'trimethylation', 'tri-methylation'], 'xrefs': [{'namespace': 'mod', 'name': 'trimethylated residue', 'identifier': '00430'}]}, 'Myr': {'synonyms': ['Myr', 'myristoylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein myristoylation', 'identifier': '0018377'}, {'namespace': 'mod', 'name': 'myristoylated residue', 'identifier': '00438'}]}, 'NGlyco': {'is_a': ['Glyco'], 'synonyms': ['NGlyco', 'N-linked glycosylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein N-linked glycosylation', 'identifier': '0006487'}, {'namespace': 'mod', 'name': 'N-glycosylated residue', 'identifier': '00006'}, {'namespace': 'mop', 'name': 'N-glycosylation', 'identifier': '0002162'}]}, 'NO': {'synonyms': ['NO', 'Nitrosylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein nitrosylation', 'identifier': '0017014'}]}, 'Nedd': {'synonyms': ['Nedd', 'neddylation', 'RUB1-protein conjugation'], 'xrefs': [{'namespace': 'go', 'name': 'protein neddylation', 'identifier': '0045116'}, {'namespace': 'mod', 'name': 'neddylated lysine', 'identifier': '01150'}]}, 'OGlyco': {'is_a': ['Glyco'], 'synonyms': ['OGlyco', 'O-linked glycosylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein O-linked glycosylation', 'identifier': '0006493'}, {'namespace': 'mod', 'name': 'O-glycosylated residue', 'identifier': '00396'}, {'namespace': 'mop', 'name': 'O-glycosylation', 'identifier': '0003162'}]}, 'Ox': {'synonyms': ['Ox', 'oxidation'], 'xrefs': [{'namespace': 'go', 'name': 'protein oxidation', 'identifier': '0018158'}]}, 'Palm': {'synonyms': ['Palm', 'palmitoylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein palmitoylation', 'identifier': '0018345'}, {'namespace': 'mod', 'name': 'palmitoylated residue', 'identifier': '00440'}]}, 'Ph': {'synonyms': ['Ph', 'phosphorylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein phosphorylation', 'identifier': '0006468'}, {'namespace': 'mod', 'identifier': '00696'}]}, 'Sulf': {'synonyms': ['Sulf', 'sulfation', 'sulphation', 'sulfur addition', 'sulphur addition', 'sulfonation', 'sulphonation'], 'target': [{'namespace': 'chebi', 'name': 'sulfo group', 'identifier': '29922'}], 'xrefs': [{'namespace': 'go', 'name': 'protein sulfation', 'identifier': '0006477'}, {'namespace': 'mod', 'name': 'sulfated residue', 'identifier': '00695'}, {'namespace': 'mop', 'name': 'sulfonation', 'identifier': '0000559'}]}, 'Sumo': {'activities': [{'namespace': 'go', 'name': 'SUMO transferase activity', 'identifier': '0019789'}], 'synonyms': ['Sumo', 'SUMOylation', 'Sumoylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein sumoylation', 'identifier': '0016925'}, {'namespace': 'mod', 'name': 'sumoylated lysine', 'identifier': '01149'}]}, 'Ub': {'synonyms': ['Ub', 'ubiquitination', 'ubiquitinylation', 'ubiquitylation'], 'xrefs': [{'namespace': 'go', 'name': 'protein ubiquitination', 'identifier': '0016567'}, {'namespace': 'mod', 'name': 'ubiquitinylated lysine', 'identifier': '01148'}, {'namespace': 'sbo', 'name': 'ubiquitination', 'identifier': '0000224'}]}, 'UbK48': {'synonyms': ['UbK48', 'Lysine 48-linked polyubiquitination'], 'xrefs': [{'namespace': 'go', 'name': 'protein K48-linked ubiquitination', 'identifier': '0070936'}]}, 'UbK63': {'synonyms': ['UbK63', 'Lysine 63-linked polyubiquitination'], 'xrefs': [{'namespace': 'go', 'name': 'protein K63-linked ubiquitination', 'identifier': '0070534'}]}, 'UbMono': {'synonyms': ['UbMono', 'monoubiquitination'], 'xrefs': [{'namespace': 'go', 'name': 'protein monoubiquitination', 'identifier': '0006513'}]}, 'UbPoly': {'synonyms': ['UbPoly', 'polyubiquitination'], 'xrefs': [{'namespace': 'go', 'name': 'protein polyubiquitination', 'identifier': '0000209'}]}}

Use Gene Ontology children of go_0006464: “cellular protein modification process”

pybel.language.pmod_legacy_labels = {'A': 'Ac', 'F': 'Farn', 'G': 'Glyco', 'H': 'Hy', 'M': 'Me', 'O': 'Ox', 'P': 'Ph', 'R': 'ADPRib', 'S': 'Sumo', 'U': 'Ub'}

A dictionary of legacy (BEL 1.0) default namespace protein modifications to their BEL 2.0 preferred value

pybel.language.gmod_namespace = {'ADPRib': 'ADPRib', 'M': 'Me', 'Me': 'Me', 'methylation': 'Me'}

A dictionary of default gene modifications. This is a PyBEL variant to the BEL specification.

pybel.language.gmod_mappings = {'ADPRib': {'synonyms': ['ADPRib'], 'xrefs': [{'namespace': 'go', 'name': 'DNA ADP-ribosylation', 'identifier': '0030592'}]}, 'Me': {'synonyms': ['Me', 'M', 'methylation'], 'xrefs': [{'namespace': 'go', 'name': 'DNA methylation', 'identifier': '0006306'}]}}

Use Gene Ontology children of go:0006304 ! “DNA modification”

class pybel.language.CitationDict(namespace, identifier, *, name=None, **kwargs)

A dictionary describing a citation.

Create a dictionary representing a reference to an entity.

Parameters

• namespace (str) – The namespace to which the entity belongs

• name (Optional[str]) – The name of the entity

• identifier (str) – The identifier of the entity in the namespace

pybel.language.citation_dict(*, namespace=None, db=None, identifier=None, db_id=None, name=None, **kwargs)

Make a citation dictionary.

Return type

CitationDict