ARCGraph (arc-validate)

ARCGraph Module

Namespace: ARCExpect
Assembly: ARCExpect.dll

Functions for creating and working with ARC FGraphs.

Types and nested modules

Type/Module	Description
Visualization	Functions for visualizing ARC FGraphs.
TermFamiliarity	Representation of the familiarity of a CvParam's CvTerm. If the CvTerm is known in, e.g., an ontology, use KnownTerm, else use UnknownTerm. ObsoleteTerm is for deprecated terms (i.e., OboTerm with `is_obsolete` = `true`).

Functions and values

Function or value	Description
`addEmptyIpsToNodeData subgraph` Full Usage: `addEmptyIpsToNodeData subgraph` Parameters: subgraph : `FGraph<string, IParam seq, ARCRelation>` Returns: `FGraph<string, IParam seq, ARCRelation>`	Takes a subgraph and adds empty IParams of the respective CvTerm to the nodedata if it is shorter than the longest IParam seq of any nodedata so that all IParam seqs have the same amount of items. Ignores the header. subgraph : `FGraph<string, IParam seq, ARCRelation>` Returns: `FGraph<string, IParam seq, ARCRelation>`
`addMissingTerms onto ips` Full Usage: `addMissingTerms onto ips` Parameters: onto : `OboOntology` ips : `IParam seq` Returns: `IParam seq`	Takes an OboOntology and a list of IParams and returns the list with all OboTerms that are missing in the list appended as empty-value IParams. onto : `OboOntology` ips : `IParam seq` Returns: `IParam seq`
`addMissingTermsInGroup ontoGraph ips` Full Usage: `addMissingTermsInGroup ontoGraph ips` Parameters: ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ips : `IParam seq` Returns: `IParam seq`	Checks if there are missing terms in a given seq of IParams by using a given ontology-based FGraph and adds them if so. A term is defined as missing if it has a part_of relation to the seq's head term and is not present in the seq's tail. ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ips : `IParam seq` Returns: `IParam seq`
`constructIntermediateMetadataSubgraph ontoGraph ips` Full Usage: `constructIntermediateMetadataSubgraph ontoGraph ips` Parameters: ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ips : `(string * TermFamiliarity seq) seq` Returns: `FGraph<string, IParam seq, ARCRelation> * (string * TermFamiliarity seq) list`	Takes an ontology-based FGraph and a seq of termname * matched IParams to create an intermediate subgraph out of it. This subgraph consists of a chain of nodes that have their termname as nodekey and their IParam seq as nodedata. The nodes are ordered by the follows-relationship taken from the ontology-based FGraph. ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ips : `(string * TermFamiliarity seq) seq` Returns: `FGraph<string, IParam seq, ARCRelation> * (string * TermFamiliarity seq) list`
`deconstructTf tf` Full Usage: `deconstructTf tf` Parameters: tf : `TermFamiliarity` Returns: `IParam`	Returns the TermFamiliarity's IParam value. tf : `TermFamiliarity` Returns: `IParam`
`fillTokenList onto tokens` Full Usage: `fillTokenList onto tokens` Parameters: onto : `OboOntology` tokens : `IParam seq` Returns: `((string * int) * IParam) seq seq seq`	Takes a structural ontology and a seq of IParams, fills in all missing IParams, and returns the IParam seq but grouped by term name (most inner seq) and divided into sections (middle seq). onto : `OboOntology` tokens : `IParam seq` Returns: `((string * int) * IParam) seq seq seq`
`fromCvParamListAsNodes cvpList` Full Usage: `fromCvParamListAsNodes cvpList` Parameters: cvpList : `CvParam list` Returns: `FGraph<(int * string), CvParam, ARCRelation>`	Takes a list of CvParams and returns the ArcGraph as an FGraph consisting of Nodes only. cvpList : `CvParam list` Returns: `FGraph<(int * string), CvParam, ARCRelation>`
`getMissingTerms onto ips` Full Usage: `getMissingTerms onto ips` Parameters: onto : `OboOntology` ips : `IParam seq` Returns: `IParam seq`	Returns all terms that are present in the given ontology but don't occur in the given CvParam list as CvParams. onto : `OboOntology` ips : `IParam seq` Returns: `IParam seq`
`getPrecedingCvParams ip graph` Full Usage: `getPrecedingCvParams ip graph` Parameters: ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * ARCRelation) seq`	Returns all preceding terms (as ID * OboTerm * ArcRelation) of a given CvParam by using a given ontology graph. ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * ARCRelation) seq`
`getRelatedIParams ip graph` Full Usage: `getRelatedIParams ip graph` Parameters: ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * ARCRelation) seq`	Returns all related terms (as ID * OboTerm * ArcRelation) of a given CvParam by using a given ontology graph. ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * ARCRelation) seq`
`getRelatedIParamsBy relating ip graph` Full Usage: `getRelatedIParamsBy relating ip graph` Parameters: relating : `FContext<string, OboTerm, ARCRelation> -> 'a` ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * 'b) seq`	Returns all terms (as ID * OboTerm * ArcRelation) of a given CvParam by using a given ontology graph via a given relating function. relating : `FContext<string, OboTerm, ARCRelation> -> 'a` ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * 'b) seq`
`getSucceedingCvParams ip graph` Full Usage: `getSucceedingCvParams ip graph` Parameters: ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * ARCRelation) seq`	Returns all succeeding terms (as ID * OboTerm * ArcRelation) of a given CvParam by using a given ontology graph. ip : `IParam` graph : `FGraph<string, OboTerm, ARCRelation>` Returns: `(string * OboTerm * ARCRelation) seq`
`groupTerms ips` Full Usage: `groupTerms ips` Parameters: ips : `IParam seq` Returns: `(string * IParam seq) seq`	Groups the given IParams by their name and groups them together. ips : `IParam seq` Returns: `(string * IParam seq) seq`
`hasFollowsTo onto currentIp priorIp` Full Usage: `hasFollowsTo onto currentIp priorIp` Parameters: onto : `FGraph<string, OboTerm, ARCRelation>` currentIp : `IParam` priorIp : `IParam` Returns: `bool`	Checks is a given current CvParam has a follows relationship to a given prior CvParam by using a given ontology graph. onto : `FGraph<string, OboTerm, ARCRelation>` currentIp : `IParam` priorIp : `IParam` Returns: `bool`
`hasPartOfTo onto currentIp priorIp` Full Usage: `hasPartOfTo onto currentIp priorIp` Parameters: onto : `FGraph<string, OboTerm, ARCRelation>` currentIp : `IParam` priorIp : `IParam` Returns: `bool`	Checks is a given current CvParam has a part_of relationship to a given prior CvParam by using a given OboOntology. onto : `FGraph<string, OboTerm, ARCRelation>` currentIp : `IParam` priorIp : `IParam` Returns: `bool`
`hasRelationTo onto relation currentIp priorIp` Full Usage: `hasRelationTo onto relation currentIp priorIp` Parameters: onto : `FGraph<string, OboTerm, ARCRelation>` relation : `ARCRelation` currentIp : `IParam` priorIp : `IParam` Returns: `bool`	Checks is a given current CvParam has a given ArcRelation to a given prior CvParam by using a given ontology graph. onto : `FGraph<string, OboTerm, ARCRelation>` relation : `ARCRelation` currentIp : `IParam` priorIp : `IParam` Returns: `bool`
`isHeader ontoGraph ip` Full Usage: `isHeader ontoGraph ip` Parameters: ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ip : `IParam` Returns: `bool`	Checks if a given IParam is a header term in a given OboOntology. ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ip : `IParam` Returns: `bool`
`isObsoleteTerm onto ip` Full Usage: `isObsoleteTerm onto ip` Parameters: onto : `OboOntology` ip : `IParam` Returns: `bool`	Checks if the given IParam contains an obsolete term using a given OboOntology. onto : `OboOntology` ip : `IParam` Returns: `bool`
`isPartOfHeader header ontoGraph ip` Full Usage: `isPartOfHeader header ontoGraph ip` Parameters: header : `IParam` ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ip : `IParam` Returns: `bool`	Checks if a given IParam has a part_of relation to a given header term using an ontology-based FGraph. header : `IParam` ontoGraph : `FGraph<string, OboTerm, ARCRelation>` ip : `IParam` Returns: `bool`
`matchTerms onto gips` Full Usage: `matchTerms onto gips` Parameters: onto : `OboOntology` gips : `(string * IParam seq) seq` Returns: `(string * TermFamiliarity seq) seq`	Takes a seq of grouped IParams and tags them according to their TermFamiliarity using a given OboOntology. onto : `OboOntology` gips : `(string * IParam seq) seq` Returns: `(string * TermFamiliarity seq) seq`
`metadataSubgraphToList subgraph` Full Usage: `metadataSubgraphToList subgraph` Parameters: subgraph : `FGraph<(string * int), IParam, ARCRelation>` Returns: `((string * int) * IParam) seq seq`	Takes a metadata subgraph and returns its content as a list of flat list in the form of (name * number) * nodedata. The inner list has their items grouped by the number. subgraph : `FGraph<(string * int), IParam, ARCRelation>` Returns: `((string * int) * IParam) seq seq`
`splitMetadataSubgraph subgraph` Full Usage: `splitMetadataSubgraph subgraph` Parameters: subgraph : `FGraph<string, IParam seq, ARCRelation>` Returns: `FGraph<(string * int), IParam, ARCRelation>`	Splits the nodedata of a given intermediate subgraph into single nodes. Nodekey changes from name to name * number (of occurence), 0-based. subgraph : `FGraph<string, IParam seq, ARCRelation>` Returns: `FGraph<(string * int), IParam, ARCRelation>`