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Hermes : terminology tools, library and microservice.

Hermes: "Herald of the gods."

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Hermes provides a set of terminology tools built around SNOMED CT including:

  • a fast terminology service with full-text search functionality; ideal for driving autocompletion in user interfaces
  • an inference engine in order to analyse SNOMED CT expressions and concepts and derive meaning
  • cross-mapping to and from other code systems
  • support for SNOMED CT compositional grammar and the SNOMED CT expression constraint language.

It is designed as both a library for embedding into larger applications and as a standalone microservice.

It is fast, both for import and for use. It imports and indexes the International and UK editions of SNOMED CT in less than 5 minutes; you can have a server running seconds after that.

It replaces previous similar tools I wrote in java and golang and is designed to fit into a wider architecture with identifier resolution, mapping and semantics as first-class abstractions.

Rather than a single monolithic terminology server, it is entirely reasonable to build multiple services, each providing an API around a specific edition or version of SNOMED CT, and to use an API gateway to manage client access. Hermes is lightweight and designed to be composed with other services.

It is part of my PatientCare v4 development; previous versions have been operational within NHS Wales since 2007.

You can have a working terminology server running by typing only a few lines at a terminal. There's no need for any special hardware, or any special dependencies such as setting up your own elasticsearch or solr cluster. You just need a filesystem! Many other tools take hours to import the SNOMED data; you'll be finished in less than 10 minutes!

A HL7 FHIR terminology facade is under development : hades. This exposes the functionality available in hermes via a FHIR terminology API. This already supports search and autocompletion using the $expand operation.

Quickstart

You can have a terminology server running in minutes. Full documentation is below, but here is a quickstart.

  1. Install clojure

e.g on Mac OS X

brew install clojure
  1. Clone the repository and change directory
git clone https://github.com/wardle/hermes
cd hermes
  1. Download and install one or more distributions

You will need to download distributions from a National Release Centre.

How to do this will principally depend on your location.

For more information, see https://www.snomed.org/snomed-ct/get-snomed. SNOMED provide a Member Licensing and Distribution Centre.

In the United States, the National Library of Medicine (NLM) has more information. For example, the SNOMED USA edition is available from https://www.nlm.nih.gov/healthit/snomedct/us_edition.html.

In the United Kingdom, you can download a distribution from NHS Digital using the TRUD service.

Hermes also provides automated downloads. Currently this is only for the UK, because I don't have access to any other national release centre. Hermes is designed with an extensible system to provide automated downloads, so could quite easily be adapted to support other release centres.

If you've downloaded a distribution manually, import like this:

clj -M:run --db snomed.db import ~/Downloads/snomed-2021/

If you're a UK user and want to use automatic downloads, you can do this

clj -M:run --db snomed.db download uk.nhs/sct-clinical api-key=trud-api-key.txt cache-dir=/tmp/trud
clj -M:run --db snomed.db download uk.nhs/sct-drug-ext api-key=trud-api-key.txt cache-dir=/tmp/trud

Ensure you have a TRUD API key.

This will download both the UK clinical edition and the UK drug extension. If you're a UK user, I'd recommend installing both.

You can download a specific edition using an ISO 6801 formatted date:

clj -M:run download uk.nhs/sct-clinical api-key trud-api-key.txt cache-dir /tmp/trud release-date 2021-03-24
clj -M:run download uk.nhs/sct-drug-ext api-key trud-api-key.txt cache-dir /tmp/trud release-date 2021-03-24

These are most useful for building reproducible container images. You can get a list of available UK versions by simply looking at the TRUD website, or using:

clj -M:run download uk.nhs/sct-clinical api-key trud-api-key.txt cache-dir /tmp/trud release-date list

My tiny i5 'NUC' machine takes 1 minute to import the UK edition of SNOMED CT and a further minute to import the UK dictionary of medicines and devices.

  1. Index and compact
clj -M:run --db snomed.db index
clj -M:run --db snomed.db compact

My machine takes 6 minutes to build the search indices and 20 seconds to compact the database.

  1. Run a server!
clj -M:run --db snomed.db --port 8080 serve

You can use hades with the 'snomed.db' index to give you a FHIR terminology server.

Common questions

What is the use of hermes?

hermes provides a simple library, and optionally a microservice, to help you make use of SNOMED CT.

A library can be embedded into your application; this is easy using Clojure or Java. You make calls using the API just as you'd use any regular library.

A microservice runs independently and you make use of the data and software by making an API call over the network.

Like all PatientCare components, you can use hermes in either way. Usually, when you're starting out, it's best to use as a library but larger projects and larger installations will want to run their software components independently, optimising for usage patterns, resilience, reliability and rate of change.

Most people who use a terminology run a server and make calls over the network.

How is this different to a national terminology service?

Previously, I implemented SNOMED CT within an EPR. Later I realised how important it was to build it as a separate module; I created terminology servers in java, and then later in golang; hermes is written in clojure. In the UK, the different health services in England and Wales have procured a national terminology server. While I support the provision of a national terminology server for convenience, I think it's important to recognise that it is the data that matters most. We need to cooperate and collaborate on semantic interoperability, but the software services that make use of those data can be centralised or distributed; when I do analytics, I can't see me making server round-trips for every check of subsumption! That would be silly; I've been using SNOMED for analytics for longer than most; you need flexibility in provisioning terminology services. I want tooling that can both provide services at scale, while is capable of running on my personal computers as well.

Unlike other available terminology servers, hermes is lightweight and has no other dependencies except a filesystem, which can be read-only when in operation. This makes it ideal for use in situations such as a data pipeline, perhaps built upon Apache Kafka - with hermes, SNOMED analytics capability can be embedded anywhere.

I don't believe in the idea of uploading codesystems and value sets in place. My approach to versioning is to run different services; I simply deploy new services and switch at the API gateway level.

Localisation

SNOMED CT is distributed across the world. The base distribution is the International release, but your local distribution will include this together with local data. Local data will include region-specific language reference sets.

The core SNOMED API relating to concepts and their meaning is not affected by issues of locale. Locale is used to derive the synonyms for any given concept. There should be a single preferred synonym for every concept in a given language reference set.

When you build a database, the search index caches the preferred synonym using the locale specified during index creation. If no locale is specified, then the system default locale will be used. In general, you should specify a locale that will match the distribution you are importing.

For example, when you are building your search index, you can use:

clj -M:run --db snomed.db --locale en-GB index  

You can specify the requested locale using IETF BCP 47, or by using a special SNOMED CT defined locale that includes the identifier of the language reference set you wish to use. I have added BCP 47 matching as an extension in hermes as the burden of managing which reference sets to use is left to the client in the SNOMED standard. Hermes tries to provide a set of sane defaults.

Note: the mapping of BCP 47 codes to a language reference set, or set of language reference sets, is easily modified. If your locale is currently unsupported, please raise an issue and it can be added easily. The current map can be found in impl/language.clj.

Such mapping is simply an extension for convenience and may not be necessary for you. You can always get the preferred synonym given a specific set of language reference sets but I find it easier to simply use 'en-GB' and let hermes do the work for me.

Can I get support?

Yes. Raise an issue, or more formal support options are available on request, including a fully-managed service.

Why are you building so many small repositories?

Small modules of functionality are easier to develop, easier to understand, easier to test and easier to maintain. I design modules to be composable so that I can stitch different components together in order to solve problems.

In larger systems, it is easy to see code rotting. Dependencies become outdated and the software becomes difficult to change easily because of software that depend on it. Small, well-defined modules are much easier to build and are less likely to need ongoing changes over time; my goal is to need to update modules only in response to changes in domain not software itself. I aim for an accretion of functionality.

It is very difficult to 'prove' software is working as designed when there are lots of moving parts.

What are you using hermes for?

I have embedded it into clinical systems; I use it for a fast autocompletion service so users start typing and the diagnosis, or procedure, or occupation, or ethnicity, or whatever, pops up. Users don't generally know they're using SNOMED CT. I use it to populate pop-ups and drop-down controls, and I use it for decision support to switch functionality on and off in my user interface - e.g. does this patient have a type of 'x' such as motor neurone disease - as well as analytics. A large number of my academic publications are as a result of using SNOMED in analytics.

What is this graph stuff you're doing?

I think health and care data are and always will be heterogeneous, incomplete and difficult to process. I do not think trying to build entities or classes representing our domain works at scale; it is fine for toy applications and trivial data modelling such as e-observations, but classes and object-orientation cannot scale across such a complete and disparate environment. Instead, I find it much easier to think about first-class properties - entity - attribute - value - and use such triples as a way of building and navigating a complex, hierarchical graph.

I am using a graph API in order to decouple subsystems and can now navigate from clinical data into different types of reference data seamlessly. For example, with the same backend data, I can view an x.500 representation of a practitioner, or a FHIR R4 Practitioner resource model. The key is to recognise that identifier resolution and mapping are first class problems within the health and care domain. Similarly, I think the semantics of reading data are very different to one of writing data. I cannot shoehorn health and care data into a REST model in which we read and write to resources representing the type. Instead, just as in real-life, we record event data which can effect change. In the end, it is all data.

Is hermes fast?

Hermes benefits from the speed of the libraries it uses, particularly Apache Lucene and lmdb, and from some fundamental design decisions including read-only operation and memory-mapped data files. It provides a HTTP server using the lightweight and reliable jetty web server.

I have a small i3 NUC server on my local wifi network, and here is an example of load testing, in which users are typing 'mnd' and expecting an autocompletion:

mark@jupiter classes % wrk -c300 -t12 -d30s --latency  'http://nuc:8080/v1/snomed/search?s=mnd'
Running 30s test @ http://nuc:8080/v1/snomed/search?s=mnd
  12 threads and 300 connections
  Thread Stats   Avg      Stdev     Max   +/- Stdev
    Latency    40.36ms   19.97ms 565.73ms   92.08%
    Req/Sec   632.19     66.79     0.85k    68.70%
  Latency Distribution
     50%   38.76ms
     75%   45.93ms
     90%   54.09ms
     99%   79.31ms
  226942 requests in 30.09s, 125.75MB read
Requests/sec:   7540.91
Transfer/sec:      4.18MB

This uses 12 threads to make 300 concurrent HTTP connections. On 99% of occasions, that would provide a fast enough response for autocompletion (<79ms). Of course, that is users typing at exactly the same time, so a single instance could support more concurrent users than that. Given its design, Hermes is designed to easily scale horizontally, because you can simply run more servers and load balance across them. Of course, these data are fairly crude, because in real-life you'll be doing more complex concurrent calls. In real deployments, I've only needed one instance for hundreds of concurrent users, but it is nice to know I can scale easily.

Can I use hermes with containers?

Yes. It is designed to be containerised, although I have a mixture of different approaches in production, including running from source code directly. I would usually advise creating a volume and populating that with data, and then permitting read-only access to your service containers. A shared volume can be memory mapped by multiple running instances and provide high scalability.

There are some examples of different configurations available.

Can I use hermes on Apple Silicon?

Yes. There are two options:

  1. Install an x86 java SDK and run using that (Rosetta). This is fast enough.

For example, you can get a list of installed JDKs:

$ /usr/libexec/java_home -V

    11.0.17 (arm64) "Amazon.com Inc." - "Amazon Corretto 11" /Users/mark/Library/Java/JavaVirtualMachines/corretto-11.0.17/Contents/Home
    11.0.14.1 (x86_64) "Azul Systems, Inc." - "Zulu 11.54.25" /Users/mark/Library/Java/JavaVirtualMachines/azul-11.0.14.1-1--x86/Contents/Home

Choose an SDK and check what we are using

$ export JAVA_HOME=$(/usr/libexec/java_home -v 11.0.14.1)
$ clj -M -e '(System/getProperty "os.arch")'

"x86_64"

  1. Build the lmdb library for your architecture (ie arm64). This is fastest.

Install the xcode command line tools, if they are not already installed

xcode-select --install

And then download lmdb and build:

git clone --depth 1 https://git.openldap.org/openldap/openldap.git
cd openldap/libraries/liblmdb
make -e SOEXT=.dylib
cp  liblmdb.dylib ~/Library/Java/Extensions

I had to ensure ~/Library/Java/Extensions existed before this step.

Once this native library is copied, you can use hermes natively using an arm64 based JDK.

$ export JAVA_HOME=$(/usr/libexec/java_home -v 11.0.17)
$ clj -M -e '(System/getProperty "os.arch")'

"aarch64"

It is likely that lmdbjava will include a pre-built lmdb binary for ARM on Mac OS X, so these steps will become unnecessary.

Documentation

A. How to download and build a terminology service

Ensure you have a pre-built jar file, or the source code checked out from github. See below for build instructions.

I'd recommend installing clojure and running using source code but use the pre-built jar file if you prefer.

1. Download and install at least one distribution.

If your local distributor is supported, hermes can do this automatically for you. Otherwise, you will need to download your local distribution(s) manually.

i) Use a registered SNOMED CT distributor to automatically download and import

There is currently only support for automatic download and import for the UK, but other distribution sources can be added if those services provide an API.

The basic command is:

clj -M:run --db snomed.db download <distribution-identifier> [properties] 

or if you are using a precompiled jar:

java -jar hermes.jar --db snomed.db download <distribution-identifier> [properties]

The distribution, as defined by distribution-identifier, will be downloaded and imported to the file-based database snomed.db.

Distribution-identifierDescription
uk.nhs/sct-clinicalUK SNOMED CT clinical - incl international release
uk.nhs/sct-drug-extUK SNOMED CT drug extension - incl dm+d

Each distribution might require custom configuration options. These can be given as key value pairs after the command, and their use will depend on which distribution you are using.

For example, the UK releases use the NHS Digital TRUD API, and so you need to pass in the following parameters:

  • api-key : path to a file containing your NHS Digital TRUD api key
  • cache-dir : directory to use for downloading and caching releases

For example, these commands will download, cache and install the International release, the UK clinical edition and the UK drug extension:

clj -M:run --db snomed.db download uk.nhs/sct-clinical api-key=trud-api-key.txt cache-dir=/tmp/trud
clj -M:run --db snomed.db download uk.nhs/sct-drug-ext api-key=trud-api-key.txt cache-dir=/tmp/trud

hermes will tell you what configuration parameters are required:

clj -M:run download uk.nhs/sct-drug-ext

Will result in:

Invalid parameters for provider ' uk.nhs/sct-drug-ext ':

should contain keys: :api-key, :cache-dir

| key        | spec    |
|============+=========|
| :api-key   | string? |
|------------+---------|
| :cache-dir | string? |

So we know we need to pass in api-key and cache-dir as above.

ii) Download and install SNOMED CT distribution file(s) manually

Depending on where you live in the World, download the most appropriate distribution(s) for your needs.

In the UK, we can obtain these from TRUD.

For example, you can download the UK "Clinical Edition", containing the International and UK clinical distributions as part of TRUD pack 26/subpack 101.

Optionally, you can also download the UK SNOMED CT drug extension, that contains the dictionary of medicines and devices (dm+d) is available as part of TRUD pack 26/subpack 105.

Once you have downloaded what you need, unzip them to a common directory and then you can use hermes to create a file-based database.

If you are running using the jar file:

java -jar hermes.jar --db snomed.db import ~/Downloads/snomed-2020

If you are running from source code:

clj -M:run --db snomed.db import ~/Downloads/snomed-2020/

The import of both International and UK distribution files takes a total of less than 3 minutes on my machine.

2. Index

For correct operation, indices are needed for components, search and reference set membership.

Run

java -jar hermes.jar --db snomed.db index

or

clj -M:run --db snomed.db index

This will build the indices; it takes about 6 minutes on my machine.

3. Compact database (optional).

This reduces the file size and takes 20 seconds. This is an optional step, but recommended.

java -jar hermes.jar --db snomed.db compact

or

clj -M:run --db snomed.db compact

Unlike prior versions, you do not need to give java more heap.

4. Run a REPL (optional)

When I first built terminology tools, either in java or in golang, I needed to also build a custom command-line interface in order to explore the ontology. This is not necessary as most developers using Clojure quickly learn the value of the REPL; a read-evaluate-print-loop in which one can issue arbitrary commands to execute. As such, one has a full Turing-complete language (a lisp) in which to explore the domain.

Run a REPL and use the terminology services interactively. I usually use a REPL from within my IDE.

clj -A:dev

5. Get the status of your installed index

You can obtain status information about any index by using:

clj -M:run --db snomed.db status

Result:

{:installed-releases
 ("SNOMED Clinical Terms version: 20220731 [R] (July 2022 Release)"
  "35.0.0_20220928000001 UK clinical extension"
  "35.1.0_20221026000001 UK drug extension"),
 :installed-locales ("en-GB" "en-US"),
 :concepts 1064775,
 :descriptions 3034620,
 :relationships 7871444,
 :refsets 530,
 :refset-items 13138061,
 :indices
 {:descriptions-concept 3034620,
  :concept-parent-relationships 4715863,
  :concept-child-relationships 4715863,
  :component-refsets 10429215,
  :associations 1246636}}

In this example, you can see I have the July 22 International release, with the UK clinical and drug extensions from September and October 22 respectively. Given that these releases have been imported, hermes recognises it can support the locales en-GB and en-US. For completeness, detailed statistics on components and indices are also provided.

6. Run a terminology web service

By default, data are returned using json, but you can request edn by simply adding "Accept:application/edn" in the request header.

java -jar hermes.jar --db snomed.db --port 8080 serve 

or

clj -M:run --db snomed.db --port 8080 serve

If you omit the serve command, or specify --help, hermes will show help text:

Usage: hermes [options] command [parameters]

Options:
  -p, --port PORT                       8080  Port number
  -a, --bind-address BIND_ADDRESS             Address to bind
      --allowed-origins "*" or ORIGINS        Set CORS policy, with "*" or comma-delimited hostnames
  -d, --db PATH                               Path to database directory
      --locale LOCALE                         Locale to use, if different from system
  -v, --verbose
  -h, --help

Commands:
 import [paths]             Import SNOMED distribution files
 list [paths]               List importable files
 download [provider] [opts] Download & install distribution from provider
 index                      Build search index.
 compact                    Compact database
 serve                      Start a terminology server
 status                     Displays status information
  • --bind-address is optional. You may want to use --bind-address 0.0.0.0
  • --allowed-origins is optional. You could use --allowed-origins "*" or --allowed-origins example.com,example.net
  • --locale sets the default locale. This is used in building your search index and as a default if clients do not specify their preference
Endpoints:

There are a range of endpoints. Here are some examples:

  • /v1/snomed/concepts/24700007 - return basic data about a single concept
  • /v1/snomed/concepts/24700007/descriptions - returns all descriptions for concept
  • /v1/snomed/concepts/24700007/preferred : returns preferred description for concept. Use an Accept-Language header to choose your locale (see below).
  • /v1/snomed/concepts/24700007/extended : returns an extended concept
  • /v1/snomed/concepts/24700007/historical - returns historical associations for this concept
  • /v1/snomed/concepts/24700007/refsets - returns refsets to which this concept is a member
  • /v1/snomed/concepts/24700007/map/999002271000000101 - crossmap to alternate codesystem (ICD-10 in this example)
  • /v1/snomed/concepts/24700007/map/991411000000109 - map into a SNOMED subset (the UK emergency unit refset in this example)
  • /v1/snomed/crossmap/999002271000000101/G35X - cross from an alternate codesystem (ICD-10 in this example)
  • /v1/snomed/search?s=mnd\&constraint=<64572001&maxHits=5 - search for a term, constrained by SNOMED ECL expression
  • /v1/snomed/expand?ecl= <19829001 AND <301867009&includeHistoric=true - expand SNOMED ECL expression
Get a single concept
http '127.0.0.1:8080/v1/snomed/concepts/24700007'
{
  "active": true,
  "definitionStatusId": 900000000000074008,
  "effectiveTime": "2002-01-31",
  "id": 24700007,
  "moduleId": 900000000000207008
}

You'll want to use the other endpoints much more frequently.

Get extended information about a single concept
http 127.0.0.1:8080/v1/snomed/concepts/24700007/extended

The result is an extended concept definition - all the information needed for inference, logic and display. For example, at the client level, we can then check whether this is a type of demyelinating disease or is a disease affecting the central nervous system without further server round-trips. Each relationship also includes the transitive closure tables for that relationship, making it easier to execute logical inference. Note how the list of descriptions includes a convenient acceptableIn and preferredIn so you can easily display the preferred term for your locale. If you provide an Accept-Language header, then you will also get a preferredDescription that is the best choice for those language preferences given what is installed.

HTTP/1.1 200 OK
Content-Type: application/json
Date: Mon, 08 Mar 2021 22:01:13 GMT

{
    "concept": {
        "active": true,
        "definitionStatusId": 900000000000074008,
        "effectiveTime": "2002-01-31",
        "id": 24700007,
        "moduleId": 900000000000207008
    },
    "descriptions": [
        {
            "acceptableIn": [],
            "active": true,
            "caseSignificanceId": 900000000000448009,
            "conceptId": 24700007,
            "effectiveTime": "2017-07-31",
            "id": 41398015,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "refsets": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "term": "Multiple sclerosis",
            "typeId": 900000000000013009
        },
        {
            "acceptableIn": [],
            "active": false,
            "caseSignificanceId": 900000000000020002,
            "conceptId": 24700007,
            "effectiveTime": "2002-01-31",
            "id": 41399011,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [],
            "refsets": [],
            "term": "Multiple sclerosis, NOS",
            "typeId": 900000000000013009
        },
        {
            "acceptableIn": [],
            "active": false,
            "caseSignificanceId": 900000000000020002,
            "conceptId": 24700007,
            "effectiveTime": "2015-01-31",
            "id": 41400016,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [],
            "refsets": [],
            "term": "Generalized multiple sclerosis",
            "typeId": 900000000000013009
        },
        {
            "acceptableIn": [],
            "active": false,
            "caseSignificanceId": 900000000000020002,
            "conceptId": 24700007,
            "effectiveTime": "2015-01-31",
            "id": 481990016,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [],
            "refsets": [],
            "term": "Generalised multiple sclerosis",
            "typeId": 900000000000013009
        },
        {
            "acceptableIn": [],
            "active": true,
            "caseSignificanceId": 900000000000448009,
            "conceptId": 24700007,
            "effectiveTime": "2017-07-31",
            "id": 754365011,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "refsets": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "term": "Multiple sclerosis (disorder)",
            "typeId": 900000000000003001
        },
        {
            "acceptableIn": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "active": true,
            "caseSignificanceId": 900000000000448009,
            "conceptId": 24700007,
            "effectiveTime": "2017-07-31",
            "id": 1223979019,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [],
            "refsets": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "term": "Disseminated sclerosis",
            "typeId": 900000000000013009
        },
        {
            "acceptableIn": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "active": true,
            "caseSignificanceId": 900000000000017005,
            "conceptId": 24700007,
            "effectiveTime": "2003-07-31",
            "id": 1223980016,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [],
            "refsets": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "term": "MS - Multiple sclerosis",
            "typeId": 900000000000013009
        },
        {
            "acceptableIn": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "active": true,
            "caseSignificanceId": 900000000000017005,
            "conceptId": 24700007,
            "effectiveTime": "2003-07-31",
            "id": 1223981017,
            "languageCode": "en",
            "moduleId": 900000000000207008,
            "preferredIn": [],
            "refsets": [
                900000000000509007,
                900000000000508004,
                999001261000000100
            ],
            "term": "DS - Disseminated sclerosis",
            "typeId": 900000000000013009
        }
    ],
    "directParentRelationships": {
        "116676008": [
            409774005,
            32693004
        ],
        "116680003": [
            6118003,
            414029004,
            39367000
        ],
        "363698007": [
            21483005
        ],
        "370135005": [
            769247005
        ]
    },
    "parentRelationships": {
        "116676008": [
            138875005,
            107669003,
            123037004,
            409774005,
            32693004,
            49755003,
            118956008
        ],
        "116680003": [
            6118003,
            138875005,
            404684003,
            123946008,
            118234003,
            128139000,
            23853001,
            246556002,
            363170005,
            64572001,
            118940003,
            414029004,
            362975008,
            363171009,
            39367000,
            80690008,
            362965005
        ],
        "363698007": [
            138875005,
            21483005,
            442083009,
            123037004,
            25087005,
            91689009,
            91723000
        ],
        "370135005": [
            138875005,
            769247005,
            308489006,
            303102005,
            281586009,
            362981000,
            719982003
        ]
    },
    "refsets": [
        991381000000107,
        999002271000000101,
        991411000000109,
        1127581000000103,
        1127601000000107,
        900000000000497000,
        447562003
    ]
}

Search

Example usage of search endpoint.

http '127.0.0.1:8080/v1/snomed/search?s=mnd\&constraint=<64572001&maxHits=5'
[
  {
    "id": 486696014,
    "conceptId": 37340000,
    "term": "MND - Motor neurone disease",
    "preferredTerm": "Motor neuron disease"
  }
]

This searches only active concepts, but both active and inactive descriptions, by default. This can be changed per request. The defaults are sensible, because a user trying to find something with a now inactive synonym such as 'Wegener's Granulomatosis' will be suprised that their search fails to return any results.

Search parameters:

  • s - the text to search
  • constraint - an ECL expression to constrain the search; I never use search without this
  • maxHits - maximum number of hits
  • inactiveConcepts - whether to search inactive concepts (default, false)
  • inactiveDescriptions - whether to search inactive descriptions (default, true)
  • fuzzy - whether to use fuzziness for search (default, false)
  • fallbackFuzzy - whether to retry using a fuzziness factor if initial search returns no results (default, false)
  • removeDuplicates - whether to remove results with the same conceptId and text (default, false)

For autocompletion, in a typical type-ahead user interface control, you might use fallbackFuzzy=1 (or fallbackFuzzy=true) and removeDuplicates=1 (or removeDuplicates=true). That will mean that if a user mistypes one or two characters, they should still get some sensible results.

Here I search for all UK medicinal products with the name amlodipine and populate my autocompletion control using the results:

http '127.0.0.1:8080/v1/snomed/search?s=amlodipine\&constraint=<10363601000001109&fallbackFuzzy=true&removeDuplicates=true&maxHits=500'

More complex expressions are supported, and no search term is actually needed.

Let's get all drugs with exactly three active ingredients:

http '127.0.0.1:8080/v1/snomed/search?constraint=<373873005|Pharmaceutical / biologic product| : [3..3]  127489000 |Has active ingredient|  = <  105590001 |Substance|'

Or, what about all disorders of the lung that are associated with oedema?

http -j '127.0.0.1:8080/v1/snomed/search?constraint= <  19829001 |Disorder of lung|  AND <  301867009 |Edema of trunk|'

The ECL can be written more concisely:

http -j '127.0.0.1:8080/v1/snomed/search?constraint= <19829001 AND <301867009'
Expanding ECL without search

If you are simply expanding an ECL expression without search terms, you can use the expand endpoint.

http -j '127.0.0.1:8080/v1/snomed/expand?ecl= <19829001 AND <301867009&includeHistoric=true'

This has an optional parameter includeHistoric which can expand the expansion to include historical associations. This is very useful in analytics.

As a concept identifier is actually a valid SNOMED ECL expression, you can do this:

http -j '127.0.0.1:8080/v1/snomed/expand?ecl=24700007&includeHistoric=true'

[
    {
        "conceptId": 586591000000100,
        "id": 1301271000000113,
        "preferredTerm": "Multiple sclerosis NOS",
        "term": "Multiple sclerosis NOS"
    },
    {
        "conceptId": 192930001,
        "id": 297181019,
        "preferredTerm": "Multiple sclerosis NOS",
        "term": "Multiple sclerosis NOS"
    },
    {
        "conceptId": 24700007,
        "id": 41398015,
        "preferredTerm": "Multiple sclerosis",
        "term": "Multiple sclerosis"
    }
    ...
]
Crossmap to and from SNOMED CT

There are endpoints for crossmapping to and from SNOMED.

Let's map one of our diagnostic terms into ICD-10:

  • 24700007 is multiple sclerosis.
  • 999002271000000101 is the ICD-10 UK complex map reference set.
http -j 127.0.0.1:8080/v1/snomed/concepts/24700007/map/999002271000000101

Result:

[
    {
        "active": true,
        "correlationId": 447561005,
        "effectiveTime": "2020-08-05",
        "id": "57433204-2371-5c6f-855f-94ff9dad7ba6",
        "mapAdvice": "ALWAYS G35.X",
        "mapCategoryId": 1,
        "mapGroup": 1,
        "mapPriority": 1,
        "mapRule": "",
        "mapTarget": "G35X",
        "moduleId": 999000031000000106,
        "referencedComponentId": 24700007,
        "refsetId": 999002271000000101
    }
]

And of course, we can crossmap back to SNOMED as well:

http -j 127.0.0.1:8080/v1/snomed/crossmap/999002271000000101/G35X

If you map a concept into a reference set that doesn't contain that concept, you'll automatically get the best parent matches instead.

Map a concept into a reference set

You will usually crossmap using a SNOMED CT crossmap reference set, such as those for ICD-10 or OPCS. However, Hermes supports crossmapping a concept into any reference set. You can use this feature in data analytics in order to reduce the dimensionality of your dataset.

Here we have multiple sclerosis (24700007), and we're mapping into the UK emergency unit reference set (991411000000109):

http -j 127.0.0.1:8080/v1/snomed/concepts/24700007/map/991411000000109

The UK emergency unit reference set gives a subset of concepts used for central reporting problems and diagnoses in UK emergency units.

As multiple sclerosis in that reference set, you'll simply get:

[
  {
    "active": true,
    "effectiveTime": "2015-10-01",
    "id": "d55ce305-3dcc-5723-8814-cd26486c37f7",
    "moduleId": 999000021000000109,
    "referencedComponentId": 24700007,
    "refsetId": 991411000000109
  }
]

But what happens if we try something that isn't in that emergency reference set?

Here is 'limbic encephalitis with LGI1 antibodies' (763794005). It isn't in that UK emergency unit reference set:

http -j 127.0.0.1:8080/v1/snomed/concepts/763794005/map/991411000000109

Result:

[
  {
    "active": true,
    "effectiveTime": "2015-10-01",
    "id": "5b3b8cdd-dd02-50e3-b207-bf4a3aa17694",
    "moduleId": 999000021000000109,
    "referencedComponentId": 45170000,
    "refsetId": 991411000000109
  }
]

You get a more general concept - 'encephalitis' (45170000) that is in the emergency unit reference set. This makes it straightforward to map concepts into subsets of terms as defined by a reference set for analytics.

You could limit users to only entering the terms in a subset, but much better to allow clinicians to regard highly-specific granular terms and be able to map to less granular terms on demand.

7. Embed into another application

You can use git coordinates in a deps.edn file, or use maven:

In your deps.edn file (make sure you change the commit-id):

[com.eldrix.hermes {:git/url "https://github.com/wardle/hermes.git"
                    :sha     "097e3094070587dc9362ca4564401a924bea952c"}

In your pom.xml:

<dependency>
  <groupId>com.eldrix</groupId>
  <artifactId>hermes</artifactId>
  <version>1.0.815</version>
</dependency>

Development

See /doc/development on how to develop, test, lint, deploy and release hermes.

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