com.eldrix.hermes.core — com.eldrix/hermes 1.0.822

Provides a terminology service, wrapping the SNOMED store and search implementations as a single unified service.

active-association-targets clj

(active-association-targets svc component-id refset-id)

Return the active association targets for a given component.

all-transitive-synonyms clj

(all-transitive-synonyms svc params)

Returns all synonyms of the specified concepts, including those of its descendants.

Parameters:

• svc : hermes service

• params : search parameters to select concepts; one of:

    - a map        : search parameters as per [[search]]
    - a string     : a string containing an ECL expression
    - a collection : a collection of concept identifiers
  

are-any? clj

(are-any? svc concept-ids parent-ids)

Are any of the concept-ids subsumed by any of the parent-ids?

Checks the is-a relationships of the concepts in question against the set of parent identifiers.

build-search-index clj deprecated

DEPRECATED: Use build-search-indices instead

build-search-indices clj deprecated

DEPRECATED: Use [[build-indices]] instead

close clj

(close svc)

compact clj

(compact root)

create-service clj

(create-service root import-from)

(create-service root import-from locale-preference-string)

Create a terminology service combining both store and search functionality in a single step. It would be unusual to use this; usually each step would be performed interactively by an end-user.

ecl-contains? clj deprecated

(ecl-contains? svc concept-ids ecl)

DEPRECATED: use intersect-ecl instead.

Do any of the concept-ids satisfy the constraint expression specified? This is an alternative to expanding the valueset and then checking membership.

expand-ecl clj

(expand-ecl svc ecl)

Expand an ECL expression.

expand-ecl-historic clj

(expand-ecl-historic svc ecl)

Expand an ECL expression and include historic associations of the results, so that the results will include now inactive/deprecated concept identifiers.

extended-refset-item clj

(extended-refset-item svc item)

Merges a map of extended attributes to the specified reference set item. The attributes will be keyed based on information from the reference set descriptor information and known field names.

get-all-children clj

(get-all-children svc concept-id)

(get-all-children svc concept-id type-id)

Return all children of the specified concept. By design, this includes the concept itself.

get-all-parents clj

(get-all-parents svc concept-id)

(get-all-parents svc concept-id type-id)

Returns all parents of the specified concept. By design, this includes the concept itself.

get-child-relationships-of-type clj

(get-child-relationships-of-type svc concept-id type-concept-id)

Returns a set of identifiers representing the child relationships of the specified type of the specified concept.

get-component-refset-ids clj

(get-component-refset-ids svc component-id)

Returns a collection of refset identifiers to which this concept is a member.

get-component-refset-items clj

(get-component-refset-items svc component-id)

(get-component-refset-items svc component-id refset-id)

Returns a sequence of refset items for the given component.

get-component-refset-items-extended clj

(get-component-refset-items-extended svc component-id)

(get-component-refset-items-extended svc component-id refset-id)

Returns a sequence of refset items for the given component, supplemented with a map of extended attributes as defined by the refset descriptor

get-concept clj

(get-concept svc concept-id)

Return the concept with the specified identifier.

get-description clj

(get-description svc description-id)

Return the description with the specified identifier.

get-descriptions clj

(get-descriptions svc concept-id)

Return a sequence of descriptions for the given concept.

get-extended-concept clj

(get-extended-concept svc concept-id)

Return an extended concept that includes the concept, its descriptions, its relationships and its refset memberships. See [[com.eldrix.hermes.snomed/ExtendedConcept]]

get-fully-specified-name clj

(get-fully-specified-name svc concept-id)

get-installed-reference-sets clj

(get-installed-reference-sets svc)

Return a set of identifiers representing installed reference sets.

get-parent-relationships clj

(get-parent-relationships svc concept-id)

Returns a map of the parent relationships keyed by type.

get-parent-relationships-expanded clj

(get-parent-relationships-expanded svc concept-id)

(get-parent-relationships-expanded svc concept-id type-id)

Returns a map of the parent relationships, with each value a set of identifiers representing the targets and their transitive closure tables. This makes it trivial to build queries that find all concepts with, for example, a common finding site at any level of granularity.

get-parent-relationships-of-type clj

(get-parent-relationships-of-type svc concept-id type-concept-id)

Returns a set of identifiers representing the parent relationships of the specified type of the specified concept.

get-preferred-synonym clj

(get-preferred-synonym svc concept-id)

(get-preferred-synonym svc concept-id language-range)

Return the preferred synonym for the concept based on the language preferences specified.

Parameters:

• svc : hermes service
• concept-id : concept identifier
• language-range : a single string containing a list of comma-separated language ranges or a list of language ranges in the form of the "Accept-Language " header defined in RFC3066.

get-reference-sets clj deprecated

(get-reference-sets svc component-id)

DEPRECATED: use get-component-refset-items instead.

get-refset-descriptor-attribute-ids clj

(get-refset-descriptor-attribute-ids svc refset-id)

Return a vector of attribute description concept ids for the given reference set.

get-refset-item clj

(get-refset-item svc uuid)

Return a specific refset item by UUID.

get-refset-members clj

(get-refset-members svc refset-id & more)

Return a set of identifiers for the members of the given refset(s).

Parameters:

• refset-id - SNOMED identifier representing the reference set.

get-relationship clj

(get-relationship svc relationship-id)

Return the relationship with the specified identifier.

get-release-information clj

(get-release-information svc)

get-status clj

(get-status root
            &
            {:keys [counts? installed-refsets?]
             :or {counts? false installed-refsets? true}})

get-synonyms clj

(get-synonyms svc concept-id)

Returns a sequence of synonyms for the given concept.

historical-associations clj

(historical-associations svc component-id)

Returns all historical-type associations for the specified component. Result is a map, keyed by the type of association (e.g. SAME-AS) and a sequence of reference set items for that association. Some concepts may be ambiguous and therefore map to multiple targets. Annoyingly, but understandably, the 'moved-to' reference set does not actually reference the new component - but the namespace to which it has moved - so for example an ancient International release may have accidentally including UK specific concepts - so they will have been removed. It is hoped that most MOVED-TO concepts will also have a SAME-AS or POSSIBLY-EQUIVALENT-TO historical association. See https://confluence.ihtsdotools.org/display/DOCRELFMT/5.2.5.1+Historical+Association+Reference+Sets and https://confluence.ihtsdotools.org/display/editorialag/Component+Moved+Elsewhere

history-profile clj

(history-profile svc profile)

Returns a set of reference sets matching the named profile. Use in conjunction with with-historical:

(with-historical svc [24700007] (history-profile :HISTORY-MIN)

See https://confluence.ihtsdotools.org/display/DOCECL/6.11+History+Supplements

import-snomed clj

(import-snomed root dirs)

Import SNOMED distribution files from the directories dirs specified into the database directory root specified.

Import is performed in three phases for each directory:

1. import of core components and essential metadata, and
2. interim indexing
3. import of non-core and extension files.

Interim indexing is necessary in order to ensure correct reification in subsequent import(s).

index clj

(index root)

(index root language-priority-list)

intersect-ecl clj

(intersect-ecl svc concept-ids ecl)

Returns a set of concept identifiers that satisfy the SNOMED ECL expression.

log-metadata clj

(log-metadata dir)

map-features clj deprecated

(map-features svc source-concept-ids target)

DEPRECATED: Use map-into instead.

map-into clj

(map-into svc source-concept-ids target)

Map the source-concept-ids into the target, usually in order to reduce the dimensionality of the dataset. Returns a set of identifiers that are in the 'target'. The target can be a collection of identifiers, an ECL expression or, for convenience, an identifier representing a reference set. The latter two will be expanded into a set of identifiers.

Parameters:

• svc : hermes service
• source-concept-ids : a collection of concept identifiers
• target : one of: - a collection of concept identifiers - an ECL expression - a refset identifier

If a source concept id resolves to multiple concepts in the target collection, then a collection will be returned such that no member of the subset is subsumed by another member.

Callers will usually need to map any source concept identifiers into their modern active replacements, if they are now inactive, as inactive source concepts do not have relationships that can be used to perform map-into.

The use of 'map-into' is in reducing the granularity of user-entered data to aid analytics. For example, rather than limiting data entry to the UK emergency reference set, a set of commonly seen diagnoses in emergency departments in the UK, we can allow clinicians to enter highly specific, granular terms, and map to the contents of that reference set as required for analytics and reporting.

For example, '991411000000109' is the UK emergency unit diagnosis refset:

(map-into svc [24700007 763794005] 991411000000109)
     =>  (#{24700007} #{45170000})

As multiple sclerosis (24700007) is in the reference set, it is returned. However, LGI1-associated limbic encephalitis (763794005) is not in the reference set, the best terms are returned ("Encephalitis" - 45170000).

This can be used to do simple classification tasks - such as determining the broad types of illness. For example, here we use ECL to define a set to include 'neurological disease', 'respiratory disease' and 'infectious disease':

(map-into svc [24700007 763794005 95883001] "118940003 OR 50043002 OR 40733004")
    => (#{118940003} #{118940003} #{40733004 118940003})

Both multiple sclerosis and LGI-1 encephalitis are types of neurological disease (118940003). However, 'Bacterial meningitis' (95883001) is mapped to both 'neurological disease' (118940003) AND 'infectious disease' (40733004).

member-field clj

(member-field svc refset-id field s)

Returns a set of referenced component identifiers that are members of the given reference set with a matching 'value' for the 'field' specified. For example, to perform a reverse map from ICD-10:

(member-field svc 447562003 "mapTarget" "G35")

member-field-prefix clj

(member-field-prefix svc refset-id field prefix)

member-field-wildcard clj

(member-field-wildcard svc refset-id field s)

Perform a member field wildcard search. Supported wildcards are *, which matches any character sequence (including the empty one), and ?, which matches any single character. '' is the escape character. Example:

    (member-field-wildcard svc 447562003 "mapTarget" "G3?")

open clj

(open root)

Open a (read-only) SNOMED service from the path root.

parse-expression clj

(parse-expression _svc s)

paths-to-root clj

(paths-to-root svc concept-id)

reverse-map clj deprecated

(reverse-map svc refset-id code)

DEPRECATED: Use member-field instead.

Returns a sequence of reference set items representing the reverse mapping from the reference set and mapTarget specified. It's almost always better to use member-field or member-field-prefix directly.

reverse-map-prefix clj deprecated

(reverse-map-prefix svc refset-id prefix)

DEPRECATED: Use member-field-prefix instead.

Returns a sequence of reference set items representing the reverse mapping from the reference set and mapTarget. It is almost always better to use member-field or member-field-prefix directly.

search clj

(search svc params)

some-indexed clj

(some-indexed pred coll)

Returns index and first logical true value of (pred x) in coll, or nil. e.g.

(some-indexed #{64572001} '(385093006 233604007 205237003 363169009 363170005 123946008 64572001 404684003 138875005))

returns: [6 664572001]

source-historical clj

(source-historical svc component-id)

(source-historical svc component-id refset-ids)

Return the requested historical associations for the component of types as defined by refset-ids, or all association refsets if omitted.

source-historical-associations clj

(source-historical-associations svc component-id)

Returns all historical-type associations in which the specified component is the target. For example, searching for 24700007 will result in a map keyed by refset-id (e.g. SAME-AS reference set) and a set of concept identifiers.

subsumed-by? clj

(subsumed-by? svc concept-id subsumer-concept-id)

with-historical clj

(with-historical svc concept-ids)

(with-historical svc concept-ids refset-ids)

For a given sequence of concept identifiers, expand to include historical associations both backwards and forwards in time.

For a currently active concept, this will return historic inactivated concepts in which it is the target. For a now inactive concept, this will return the active associations and their historic associations.

By default, all types of historical associations except MoveTo and MovedFrom are included, but this is configurable.