Module: bbop-graph-noctua

Purpose: Noctua editing operations ove a bbop-graph base. The base pieces are just subclasses of their analogs in bbop-graph. Now, a discussion if the structure an terminology of the evidence model. Definitions: - "model": the graph model as a whole - "seed": an evidence instance that is referenced ; a seed may only belong to a single clique - "sub_clique": the evidence subgraph pattern built off of a seed - "clique" the complete evidence subgraph, obtained by walking all edges from any node in it (should be same no matter what node) - "shared_struct": (currently) nodes of the clique that may be shared between different sub_cliques; for now, just pmid nodes Rules: A clique may only be removed from the graph, with its constitutent sub_cliques contained as referenced subgraphs, when: - all constituent sub_cliques have the "correct" structure - all clique nodes are in at least one sub_clique - sub_cliques only share structure in shared_struct nodes
Source:
See:
  • module:bbop-graph

Classes

annotation
violation

Methods

(inner) add_annotation(in_ann) → {Array}

Add annotation.
Parameters:
Name Type Description
in_ann annotation annotation to add
Source:
Returns:
list of all annotations
Type
Array

(inner) add_referenced_subgraph(subgraph) → {Array}

Add referenced subgraph.
Parameters:
Name Type Description
subgraph graph subgraph to add
Source:
Returns:
list of all subgraphs
Type
Array

(inner) annotations(in_annsopt) → {Array}

Get/set annotation list.
Parameters:
Name Type Attributes Description
in_anns Array <optional>
 list of annotations to clobber current list
Source:
Returns:
list of all annotations
Type
Array

(inner) get_annotations_by_filter(filter) → {Array}

Get a sublist of annotation using the filter function. The filter function take a single annotation as an argument, and adds to the return list if it evaluates to true.
Parameters:
Name Type Description
filter function function described above
Source:
Returns:
list of passing annotations
Type
Array

(inner) get_annotations_by_id(aid) → {Array}

Get sublist of annotations with a certain ID.
Parameters:
Name Type Description
aid String annotation ID to look for
Source:
Returns:
list of list of annotations with that ID
Type
Array

(inner) get_annotations_by_key(key) → {Array}

Get sublist of annotations with a certain key.
Parameters:
Name Type Description
key String key to look for.
Source:
Returns:
list of list of annotations with that key
Type
Array

(inner) get_basic_evidence(annotation_ids) → {Array}

Returns a list with the following structure: : [ { id: , : cls: , : source: , : date: , : etc : }, : ... : ] Each top-level element in the list represents the core information in a simple (GO-style) element. This is essentially a distilled version of get_referenced_individual_profiles for cases where that is modelling simple piece of evidence (single non-nested class expression and a set know list of annotations).
Parameters:
Name Type Description
annotation_ids Array list of strings that identify the annotation keys that will be captured--
Source:
Returns:
list of referenced_individual simple evidence information.
Type
Array

(inner) get_referenced_subgraph_by_id(iid) → {Object|null}

Get a referenced_subgraph with a certain ID.
Parameters:
Name Type Description
iid String referenced_individual ID to look for
Source:
Returns:
referenced_subgraph with that ID
Type
Object | null

(inner) get_referenced_subgraph_profiles(extractoropt) → {Array}

Returns a list with the following structure: : [ { id: , : class_expressions: [{class_expression}, ...], : anntations: [{annotation}, ...] }, : ... : ] Each top-level element in the list represents the core information of a single referenced graph for a node or edge in this model. Keep in mind that this may be most useful in the GO Noctua use case as reference subgraphs with singleton elements, where the class(es) are evidence and the annotations keep things such as source (e.g. PMID), etc.
Parameters:
Name Type Attributes Description
extractor function <optional>
 extraction functions to use instead of default
Source:
Returns:
list of referenced_individual information
Type
Array

(inner) get_referenced_subgraphs_by_filter(filter) → {Array}

Get a sublist of referenced subgraphs using the filter function. The filter function take a single subgraph as an argument, and adds it to the return list if it evaluates to true.
Parameters:
Name Type Description
filter function function described above
Source:
Returns:
list of passing subgraphs
Type
Array

(inner) referenced_subgraph(subgraphsopt) → {Array}

Get/set referenced subgraph list. Copies in new data.
Parameters:
Name Type Attributes Description
subgraphs Array <optional>
 list of {graph} to clobber current list
Source:
Returns:
list of all referenced subgraphs
Type
Array