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com.eldrix.hermes.core

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

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

active-association-targetsclj

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

Return the active association targets for a given component.

Return the active association targets for a given component.
sourceraw docstring

all-transitive-synonymsclj

(all-transitive-synonyms svc params)

Returns all of the 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
Returns all of the 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
sourceraw docstring

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.

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.
sourceraw docstring

build-search-indexclj

(build-search-index root)
(build-search-index root language-priority-list)
source

closeclj

(close svc)
source

compactclj

(compact root)
source

create-serviceclj

(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.

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.
sourceraw docstring

ecl-contains?clj

(ecl-contains? svc concept-ids ecl)

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

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

expand-eclclj

(expand-ecl svc ecl)

Expand an ECL expression.

Expand an ECL expression.
sourceraw docstring

expand-ecl-historicclj

(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.

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

get-all-childrenclj

(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.

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

get-all-parentsclj

(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.

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

get-child-relationships-of-typeclj

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

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

Returns a collection of identifiers representing the child relationships of
the specified type of the specified concept.
sourceraw docstring

get-component-refset-idsclj

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

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

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

get-component-refset-itemsclj

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

get-conceptclj

(get-concept svc concept-id)

Return the concept with the specified identifier.

Return the concept with the specified identifier.
sourceraw docstring

get-descriptionsclj

(get-descriptions svc concept-id)
source

get-extended-conceptclj

(get-extended-concept svc concept-id)
source

get-fully-specified-nameclj

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

get-installed-reference-setsclj

(get-installed-reference-sets svc)
source

get-parent-relationships-of-typeclj

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

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

Returns a collection of identifiers representing the parent relationships of
the specified type of the specified concept.
sourceraw docstring

get-preferred-synonymclj

(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.
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.
sourceraw docstring

get-reference-setscljdeprecated

(get-reference-sets svc component-id)

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

DEPRECATED: use [[get-component-refset-items]] instead.
sourceraw docstring

get-refset-itemclj

(get-refset-item svc uuid)
source

get-refset-membersclj

(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.
Return a set of identifiers for the members of the given refset(s).
Parameters:
- refset-id  - SNOMED identifier representing the reference set.
sourceraw docstring

get-release-informationclj

(get-release-information svc)
source

get-statusclj

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

get-synonymsclj

(get-synonyms svc concept-id)

Returns a collection of synonyms for the given concept.

Returns a collection of synonyms for the given concept.
sourceraw docstring

historical-associationsclj

(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

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
sourceraw docstring

import-snomedclj

(import-snomed root dirs)

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

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

log-metadataclj

(log-metadata dir)
source

map-featurescljdeprecated

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

DEPRECATED: Use map-into instead.

DEPRECATED: Use [[map-into]] instead.
sourceraw docstring

map-intoclj

(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.

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.

It would be usual to map any source concept identifiers into their modern active replacements, if they are now inactive.

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).

Map the source-concept-ids into the target, usually in order to reduce the
dimensionality of the dataset.

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.

It would be usual to map any source concept identifiers into their modern
active replacements, if they are now inactive.

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).
sourceraw docstring

openclj

(open root)
(open root {:keys [quiet?] :or {quiet? false}})

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

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

parse-expressionclj

(parse-expression svc s)
source

paths-to-rootclj

(paths-to-root svc concept-id)
source

reverse-mapclj

(reverse-map svc refset-id code)

Returns the reverse mapping from the reference set and mapTarget specified.

Returns the reverse mapping from the reference set and mapTarget specified.
sourceraw docstring

reverse-map-rangeclj

(reverse-map-range svc refset-id prefix)
(reverse-map-range svc refset-id lower-bound upper-bound)

Returns the reverse mapping from the reference set specified, performing what is essentially a prefix search using the parameters.

Returns the reverse mapping from the reference set specified, performing
what is essentially a prefix search using the parameters.
sourceraw docstring

(search svc params)
source

some-indexedclj

(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]

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]`
sourceraw docstring

source-historicalclj

(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 assoc-refset-ids, or all association refsets if omitted.

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

source-historical-associationsclj

(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.

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.
sourceraw docstring

subsumed-by?clj

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

with-historicalclj

(with-historical svc concept-ids)
(with-historical svc concept-ids assoc-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.

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. 
sourceraw docstring

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