Constants

Constants for PyBEL.

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

pybel.constants.get_cache_connection()[source]

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.DIRECTLY_REGULATES = 'directlyRegulates'

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.CAUSAL_APOLAR_RELATIONS = {'directlyRegulates', 'regulates'}

A set of all causal relationships that have an inderminate polarity

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

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', 'directlyRegulates', '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]

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)[source]

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: str

The entity’s namespace.

Return type

str

property name: str

The entity’s name or label.

Return type

str

property identifier: str

The entity’s identifier.

Return type

str

property curie: str

Return this entity as a CURIE.

Return type

str

property obo: str

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)[source]

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)[source]

Make a citation dictionary.

Return type

CitationDict