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.
Check the environment variable
PYBEL_CONNECTION
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 variablePYBEL_CONFIG_DIRECTORY
has been set.Return a default connection string using a SQLite database in the
~/.pybel
. Optionally, this directory might be in a different place if the environment variablePYBEL_RESOURCE_DIRECTORY
has been set.
- Return type
-
pybel.constants.
BEL_DEFAULT_NAMESPACE
= 'bel'¶ The default namespace given to entities in the BEL language
-
pybel.constants.
CITATION_TYPES
= {'Book': None, 'DOI': 'doi', 'Journal': None, 'Online Resource': None, 'Other': None, 'PubMed': 'pmid', 'PubMed Central': 'pmc', 'URL': None}¶ The valid citation types .. seealso:: https://wiki.openbel.org/display/BELNA/Citation
-
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_DB
= 'db'¶ Represents the key for the citation type in a citation dictionary
-
pybel.constants.
CITATION_IDENTIFIER
= 'db_id'¶ Represents the key for the citation reference in a citation dictionary
-
pybel.constants.
CITATION_DB_NAME
= 'db_name'¶ Represents the key for the optional PyBEL citation title entry in a citation dictionary
-
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
= 'db_name'¶ 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.
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.
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.
SUBJECT
= 'subject'¶ The key for an internal edge data dictionary for the subject modifier dictionary
-
pybel.constants.
OBJECT
= 'object'¶ The key for an internal edge data dictionary for the object 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', 'object', 'relation', 'subject'}¶ 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', 'object', 'relation', 'subject'}¶ 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'¶
-
pybel.constants.
TRANSLATED_TO
= 'translatedTo'¶
-
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 thepybel.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 thepybel.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]
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pybel.constants.
METADATA_AUTHORS
= 'authors'¶ The key for the document authors. Can be accessed by
graph.document[METADATA_NAME]
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pybel.constants.
METADATA_CONTACT
= 'contact'¶ The key for the document contact email. Can be accessed by
graph.document[METADATA_CONTACT]
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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]
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pybel.constants.
METADATA_PROJECT
= 'project'¶ The key for the document project. Can be accessed by
graph.document[METADATA_PROJECT]
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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
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pybel.constants.
METADATA_INSERT_KEYS
= {'authors', 'contact', 'copyright', 'description', 'disclaimer', 'licenses', 'name', 'version'}¶ The keys to use when inserting a graph to the cache
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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
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pybel.constants.
REQUIRED_METADATA
= {'authors', 'contact', 'description', 'name', 'version'}¶ A set representing the required metadata during BEL document parsing
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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
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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
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pybel.constants.
GMOD_ORDER
= ['kind', 'identifier']¶ The order for serializing gene modification data
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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
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pybel.constants.
GSUB_VARIANT
= 'variant'¶ The key for the effect of a gene substitution. Only used during parsing since this is converted to HGVS
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pybel.constants.
PMOD_CODE
= 'code'¶ The key for the protein modification code.
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pybel.constants.
PMOD_POSITION
= 'pos'¶ The key for the protein modification position.
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pybel.constants.
PMOD_ORDER
= ['kind', 'identifier', 'code', 'pos']¶ The order for serializing information about a protein modification
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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
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pybel.constants.
PSUB_POSITION
= 'position'¶ The key for the position of a protein substitution. Only used during parsing since this is converted to HGVS.
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pybel.constants.
PSUB_VARIANT
= 'variant'¶ The key for the variant of a protein substitution.Only used during parsing since this is converted to HGVS.
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pybel.constants.
TRUNCATION_POSITION
= 'position'¶ The key for the position at which a protein is truncated
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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
-
pybel.constants.
DEFAULT_SERVICE_URL
= 'https://bel-commons.scai.fraunhofer.de'¶ The default location of PyBEL Web
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
-
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))
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pybel.language.
activity_mapping
= {'cat': {'identifier': 'GO:0003824', 'name': 'catalytic activity', 'namespace': 'GO'}, 'chap': {'identifier': 'GO:0044183', 'name': 'protein binding involved in protein folding', 'namespace': 'GO'}, 'gap': {'identifier': 'GO:0032794', 'name': 'GTPase activating protein binding', 'namespace': 'GO'}, 'gef': {'identifier': 'GO:0005085', 'name': 'guanyl-nucleotide exchange factor activity', 'namespace': 'GO'}, 'gtp': {'identifier': 'GO:0005525', 'name': 'GTP binding', 'namespace': 'GO'}, 'kin': {'identifier': 'GO:0016301', 'name': 'kinase activity', 'namespace': 'GO'}, 'molecularActivity': {'identifier': 'GO:0003674', 'name': 'molecular_function', 'namespace': 'GO'}, 'pep': {'identifier': 'GO:0008233', 'name': 'peptidase activity', 'namespace': 'GO'}, 'phos': {'identifier': 'GO:0016791', 'name': 'phosphatase activity', 'namespace': 'GO'}, 'ribo': {'identifier': 'GO:0003956', 'name': 'NAD(P)+-protein-arginine ADP-ribosyltransferase activity', 'namespace': 'GO'}, 'tport': {'identifier': 'GO:0005215', 'name': 'transporter activity', 'namespace': 'GO'}, 'tscript': {'identifier': 'GO:0001071', 'name': 'nucleic acid binding transcription factor activity', 'namespace': 'GO'}}¶ Maps the default BEL molecular activities to Gene Ontology Molecular Functions
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pybel.language.
compartment_mapping
= {'cell surface': {'identifier': 'GO:0009986', 'name': 'cell surface', 'namespace': 'GO'}, 'cytoplasm': {'identifier': 'GO:0005737', 'name': 'cytoplasm', 'namespace': 'GO'}, 'extracellular space': {'identifier': 'GO:0005615', 'name': 'extracellular space', 'namespace': 'GO'}, 'intracellular': {'identifier': 'GO:0005622', 'name': 'intracellular', 'namespace': 'GO'}, 'nucleus': {'identifier': 'GO:0005634', 'name': 'nucleus', 'namespace': 'GO'}}¶ Maps the default BEL cellular components to Gene Ontology Cellular Components
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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
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pybel.language.
abundance_sbo_mapping
= {'BiologicalProcess': {'identifier': 'SBO:0000375', 'name': 'process', 'namespace': 'SBO'}, 'Complex': {'identifier': 'SBO:0000297', 'name': 'protein complex', 'namespace': 'SBO'}, 'Gene': {'identifier': 'SBO:0000243', 'name': 'gene', 'namespace': 'SBO'}, 'Pathology': {'identifier': 'SBO:0000358', 'name': 'phenotype', 'namespace': 'SBO'}, 'RNA': {'identifier': 'SBO:0000278', 'name': 'messenger RNA', 'namespace': 'SBO'}, 'miRNA': {'identifier': 'SBO:0000316', 'name': 'microRNA', 'namespace': 'SBO'}}¶ Maps the BEL abundance types to the Systems Biology Ontology
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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': 'GO:0006471'}, {'namespace': 'MOD', 'name': 'adenosine diphosphoribosyl (ADP-ribosyl) modified residue', 'identifier': 'MOD:00752'}, {'namespace': 'MOP', 'name': 'adenosinediphosphoribosylation', 'identifier': 'MOP:0000220'}]}, 'Ac': {'synonyms': ['Ac', 'acetylation'], 'xrefs': [{'namespace': 'SBO', 'name': 'acetylation', 'identifier': 'SBO:0000215'}, {'namespace': 'GO', 'name': 'protein acetylation', 'identifier': 'GO:0006473'}, {'namespace': 'MOD', 'name': 'acetylated residue', 'identifier': 'MOD:00394'}, {'namespace': 'MOP', 'name': 'acetylation', 'identifier': 'MOP:0000030'}]}, 'Farn': {'synonyms': ['Farn', 'farnesylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein farnesylation', 'identifier': 'GO:0018343'}, {'namespace': 'MOD', 'name': 'farnesylated residue', 'identifier': 'MOD:00437'}, {'namespace': 'MOP', 'name': 'farnesylation', 'identifier': 'MOP:0000429'}]}, 'Gerger': {'synonyms': ['Gerger', 'geranylgeranylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein geranylgeranylation', 'identifier': 'GO:0018344'}, {'namespace': 'MOD', 'name': 'geranylgeranylated residue ', 'identifier': 'MOD:00441'}, {'namespace': 'MOP', 'name': 'geranylgeranylation', 'identifier': 'MOP:0000431'}]}, 'Glyco': {'synonyms': ['Glyco', 'glycosylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein glycosylation', 'identifier': 'GO:0006486'}, {'namespace': 'MOD', 'name': 'glycosylated residue', 'identifier': 'MOD:00693'}, {'namespace': 'MOP', 'name': 'glycosylation', 'identifier': 'MOP:0000162'}]}, 'Hy': {'synonyms': ['Hyhydroxylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein hydroxylation', 'identifier': 'GO:0018126'}, {'namespace': 'MOD', 'name': 'hydroxylated residue', 'identifier': 'MOD:00677'}, {'namespace': 'MOP', 'name': 'hydroxylation', 'identifier': 'MOP:0000673'}]}, 'ISG': {'activities': [{'namespace': 'GO', 'name': 'ISG15 transferase activity', 'identifier': 'GO:0042296'}], 'synonyms': ['ISG', 'ISGylation', 'ISG15-protein conjugation'], 'xrefs': [{'namespace': 'GO', 'name': 'ISG15-protein conjugation', 'identifier': 'GO:0032020'}]}, 'Me': {'synonyms': ['Me', 'methylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein methylation', 'identifier': 'GO:0006479'}, {'namespace': 'MOD', 'name': 'methylated residue', 'identifier': 'MOD:00427'}]}, 'Me1': {'is_a': ['Me'], 'synonyms': ['Me1', 'monomethylation', 'mono-methylation'], 'xrefs': [{'namespace': 'MOD', 'name': 'monomethylated residue', 'identifier': 'MOD:00599'}]}, 'Me2': {'is_a': ['Me'], 'synonyms': ['Me2', 'dimethylation', 'di-methylation'], 'xrefs': [{'namespace': 'MOD', 'name': 'dimethylated residue', 'identifier': 'MOD:00429'}]}, 'Me3': {'is_a': ['Me'], 'synonyms': ['Me3', 'trimethylation', 'tri-methylation'], 'xrefs': [{'namespace': 'MOD', 'name': 'trimethylated residue', 'identifier': 'MOD:00430'}]}, 'Myr': {'synonyms': ['Myr', 'myristoylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein myristoylation', 'identifier': 'GO:0018377'}, {'namespace': 'MOD', 'name': 'myristoylated residue', 'identifier': 'MOD:00438'}]}, 'NGlyco': {'is_a': ['Glyco'], 'synonyms': ['NGlyco', 'N-linked glycosylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein N-linked glycosylation', 'identifier': 'GO:0006487'}, {'namespace': 'MOD', 'name': 'N-glycosylated residue', 'identifier': 'MOD:00006'}, {'namespace': 'MOP', 'name': 'N-glycosylation', 'identifier': 'MOP:0002162'}]}, 'NO': {'synonyms': ['NO', 'Nitrosylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein nitrosylation', 'identifier': 'GO:0017014'}]}, 'Nedd': {'synonyms': ['Nedd', 'neddylation', 'RUB1-protein conjugation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein neddylation', 'identifier': 'GO:0045116'}, {'namespace': 'MOD', 'name': 'neddylated lysine', 'identifier': 'MOD:01150'}]}, 'OGlyco': {'is_a': ['Glyco'], 'synonyms': ['OGlyco', 'O-linked glycosylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein O-linked glycosylation', 'identifier': 'GO:0006493'}, {'namespace': 'MOD', 'name': 'O-glycosylated residue', 'identifier': 'MOD:00396'}, {'namespace': 'MOP', 'name': 'O-glycosylation', 'identifier': 'MOP:0003162'}]}, 'Ox': {'synonyms': ['Ox', 'oxidation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein oxidation', 'identifier': 'GO:0018158'}]}, 'Palm': {'synonyms': ['Palm', 'palmitoylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein palmitoylation', 'identifier': 'GO:0018345'}, {'namespace': 'MOD', 'name': 'palmitoylated residue', 'identifier': 'MOD:00440'}]}, 'Ph': {'synonyms': ['Ph', 'phosphorylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein phosphorylation', 'identifier': 'GO:0006468'}, {'namespace': 'MOD', 'identifier': 'MOD:00696'}]}, 'Sulf': {'synonyms': ['Sulf', 'sulfation', 'sulphation', 'sulfur addition', 'sulphur addition', 'sulfonation', 'sulphonation'], 'target': [{'namespace': 'CHEBI', 'name': 'sulfo group', 'identifier': 'CHEBI:29922'}], 'xrefs': [{'namespace': 'GO', 'name': 'protein sulfation', 'identifier': 'GO:0006477'}, {'namespace': 'MOD', 'name': 'sulfated residue', 'identifier': 'MOD:00695'}, {'namespace': 'MOP', 'name': 'sulfonation', 'identifier': 'MOP:0000559'}]}, 'Sumo': {'activities': [{'namespace': 'GO', 'name': 'SUMO transferase activity', 'identifier': 'GO:0019789'}], 'synonyms': ['Sumo', 'SUMOylation', 'Sumoylation'], 'xrefs': [{'namespace': 'GO', 'name': 'protein sumoylation', 'identifier': 'GO:0016925'}, {'namespace': 'MOD', 'name': 'sumoylated lysine', 'identifier': 'MOD:01149'}]}, 'Ub': {'synonyms': ['Ub', 'ubiquitination', 'ubiquitinylation', 'ubiquitylation'], 'xrefs': [{'namespace': 'SBO', 'name': 'ubiquitination', 'identifier': 'SBO:0000224'}, {'namespace': 'GO', 'name': 'protein ubiquitination', 'identifier': 'GO:0016567'}, {'namespace': 'MOD', 'name': 'ubiquitinylated lysine', 'identifier': 'MOD:01148'}]}, 'UbK48': {'synonyms': ['UbK48', 'Lysine 48-linked polyubiquitination'], 'xrefs': [{'namespace': 'GO', 'name': 'protein K48-linked ubiquitination', 'identifier': 'GO:0070936'}]}, 'UbK63': {'synonyms': ['UbK63', 'Lysine 63-linked polyubiquitination'], 'xrefs': [{'namespace': 'GO', 'name': 'protein K63-linked ubiquitination', 'identifier': 'GO:0070534'}]}, 'UbMono': {'synonyms': ['UbMono', 'monoubiquitination'], 'xrefs': [{'namespace': 'GO', 'name': 'protein monoubiquitination', 'identifier': 'GO:0006513'}]}, 'UbPoly': {'synonyms': ['UbPoly', 'polyubiquitination'], 'xrefs': [{'namespace': 'GO', 'name': 'protein polyubiquitination', 'identifier': 'GO:0000209'}]}}¶ Use Gene Ontology children of GO_0006464: “cellular protein modification process”
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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
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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.
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pybel.language.
gmod_mappings
= {'ADPRib': {'synonyms': ['ADPRib'], 'xrefs': [{'namespace': 'GO', 'name': 'DNA ADP-ribosylation', 'identifier': 'GO:0030592'}]}, 'Me': {'synonyms': ['Me', 'M', 'methylation'], 'xrefs': [{'namespace': 'GO', 'name': 'DNA methylation', 'identifier': 'GO:0006306'}]}}¶ Use Gene Ontology children of GO_0006304: “DNA modification”