Natural language (indra.assemblers.english.assembler)

class indra.assemblers.english.assembler.AgentWithCoordinates(agent_str, name, db_refs, coords=None)

English representation of an agent.

Parameters:

• agent_str (str) – Full English description of an agent.
• name (str) – Name of an agent.
• db_refs (dict) – Dictionary of database identifiers associated with this agent.
• coords (tuple(int)) – A tuple of integers representing coordinates of agent name in a text. If not provided, coords will be set to coordinates of name in agent_str. When AgentWithCoordinates is a part of SentenceBuilder or EnglishAssembler, the coords represent the location of agent name in the SentenceBuilder.sentence or EnglishAssembler.model.

update_coords(shift_by)

Update coordinates by shifting them by a given number of characters.

Parameters:shift_by (int) – How many characters to shift the parameters by.

class indra.assemblers.english.assembler.EnglishAssembler(stmts=None)

This assembler generates English sentences from INDRA Statements.

Parameters:stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be added to the assembler.

statements

A list of INDRA Statements to assemble.

Type:list[indra.statements.Statement]

model

The assembled sentences as a single string.

Type:str

stmt_agents

A list containing lists of AgentWithCoordinates objects for each of the assembled statements. Coordinates represent the location of agents in the model.

Type:list[list[AgentWithCoordinates]]

add_statements(stmts)

Add INDRA Statements to the assembler’s list of statements.

Parameters:stmts (list[indra.statements.Statement]) – A list of indra.statements.Statement to be added to the statement list of the assembler.

make_model()

Assemble text from the set of collected INDRA Statements.

Returns:stmt_strs – Return the assembled text as unicode string. By default, the text is a single string consisting of one or more sentences with periods at the end. Return type:str

class indra.assemblers.english.assembler.SentenceBuilder

Builds a sentence from agents and strings.

agents

A list of AgentWithCoordinates objects that are part of a sentence. The coordinates of the agent name are being dynamically updated as the sentence is being constructed.

Type:list[AgentWithCoordinates]

sentence

A sentence that is being built by the builder.

Type:str

append(element)

Append an element to the end of the sentence.

Parameters:element (str or AgentWithCoordinates) – A string or AgentWithCoordinates object to be appended in the end of the sentence. Agent’s name coordinates are updated relative to the current length of the sentence.

append_as_list(lst, oxford=True)

Append a list of elements in a gramatically correct way.

Parameters:

• lst (list[str] or list[AgentWithCoordinates]) – A list of elements to append. Elements in this list represent a sequence and grammar standards require the use of appropriate punctuation and conjunction to connect them (e.g. [ag1, ag2, ag3]).
• oxford (Optional[bool]) – Whether to use oxford grammar standards. Default: True

append_as_sentence(lst)

Append a list of elements by concatenating them together.

Note: a list of elements here are parts of sentence that do not represent a sequence and do not need to have extra punctuation or conjunction between them.

Parameters:lst (list[str] or list[AgentWithCoordinates]) – A list of elements to append. Elements in this list do not represent a sequence and do not need to have extra punctuation or conjunction between them (e.g. [subj, ‘ is a GAP for ‘, obj]).

make_sentence()

After the parts of a sentence are joined, create a sentence.

prepend(element)

Prepend an element to the beginning of the sentence.

Parameters:element (str or AgentWithCoordinates) – A string or AgentWithCoordinates object to be added in the beginning of the sentence. All existing agents’ names coordinates are updated relative to the new length of the sentence.

indra.assemblers.english.assembler.english_join(lst)

Join a list of strings according to English grammar.

Parameters:lst (list of str) – A list of strings to join. Returns:A string which describes the list of elements, e.g., “apples, pears, and bananas”. Return type:str

indra.assemblers.english.assembler.statement_base_verb(stmt_type)

Return the base verb form of a statement type.

Parameters:stmt_type (str) – The lower case string form of a statement type, for instance, ‘phosphorylation’. Returns:The base verb form of a statement type, for instance, ‘phosphorylate’. Return type:str

indra.assemblers.english.assembler.statement_passive_verb(stmt_type)

Return the passive / state verb form of a statement type.

Parameters:stmt_type (str) – The lower case string form of a statement type, for instance, ‘phosphorylation’. Returns:The passive/state verb form of a statement type, for instance, ‘phosphorylated’. Return type:str

indra.assemblers.english.assembler.statement_present_verb(stmt_type)

Return the present verb form of a statement type.

Parameters:stmt_type (str) – The lower case string form of a statement type, for instance, ‘phosphorylation’. Returns:The present verb form of a statement type, for instance, ‘phosphorylates’. Return type:str