BodyPartIndex.ts

Provides data and simple libraries for manipulating a standard list of anatomic locations (see https://www.anatomiclocations.org).

Installation

npm i @talkasab/body_part_index

BodyPartIndex (Scenarios)

How to open the library?

To open the library, you first need to import it into your project. Then, you can use the BodyPartIndex object.

import { BodyPartIndex } from '@talkasab/body_part_index';

const index = new BodyPartIndex();

How to use a local JSON file of body parts?

The packages comes bundled with a version of the body part database as a JSON file, which it loads by default. To initialize a BodyPartIndex object with a local JSON file (with the same structure), separately load/parse the file, and pass the resulting JSON as the bodyPartData property of a configuration object to the constructor.

const fs = require('fs')
const bodyPartsJson = JSON.parse(fs.readFileSync('localBodyPartData.json', 'utf8'));
const index = new BodyPartIndex({bodyPartData: bodyPartsJson});

How to add local codes?

To add local codes to the library, you need to pass a JSON with the data linking the code to the radlexId as the localBodyPartMappings to a configuration object as an argument to the constructor.

const index = new BodyPartIndex({
    localBodyPartMappings: [
        {

            localCode: {
                code: '3110',
                system: 'StElsewhere'
            },
            radlexId: 'RID56'
        },
        {

            localCode: {
                code: '31129',
                system: 'StElsewhere'
            },
            radlexId: 'RID905'
        }
    ]
});

How to get a particular body part by RadLex ID, SNOMED, or another code?

To get a body part by id or any code (include local codes), you need to use the get function.

const index = new BodyPartIndex({
    localBodyPartMappings: [
        { 
            localCode: { 
                code: 'THX1138', 
                system: 'LOCAL' 
            }, 
            radlexId: 'RID294' 
        }
    ]
});
const bodyPart = index.get('RID294');
const bodyPart2 = index.get('265256');  // FMA code
const bodyPart3 = index.get('THX1138'); // Local code

This function returns a BodyPart object.

How to get a particular body part by code and system?

To get a body part by code AND system, you need to use the getByCodeAndSystem function.

const index = new BodyPartIndex();
const bodyPart = index.getByCodeAndSystem({
    code: '443167003',
    system: 'SNOMED'
});

This function returns a BodyPart object.

How to search for body parts based on names or synonyms?

The search function will return all the BodyParts that match a specific search value.

const index = new BodyPartIndex();
const bodyParts = index.search('adnexa');

BodyPart (Scenarios)

What can you get from a BodyPart?

const index = new BodyPartIndex();
const bodyPart = index.get('RID294');
bodyPart?.getDescription(); // "uterine adnexa"
bodyPart?.getSexSpecific(); // "Female"
bodyPart?.getSynonyms(); // ["adnexa"]
bodyPart?.getContainedBy(); // BodyPart object; RID2507, pelvis
bodyPart?.getPartOf(); // BodyPart object; RID270, female genital system
bodyPart?.getCodes(); // Array of Codes; [ {"system": "SNOMED", "code": "53065001"}, ... ]

How do deal with sided body parts?

For cases where the body part is sided, the index contains three versions: an unsided version, a left-sided version, and a right-sided version. All of these are aware of each other.

const index = new BodyPartIndex();
const bodyPart = index.get('RID294'); // uterine adnexa (side not specified)
// From the unsided version, get the right- and left-sided versions
const right = bodyPart?.getRight(); // BodyPart object; RID294_RID5825, right uterine adnexa
const left = bodyPart?.getLeft(); // BodyPart object; RID294_RID5824, left uterine adnexa
// From either of the sided versions, can get back to the unsided or to the other side
bodyPart?.isEqual(right?.getUnsided()); // true
right?.isEqual(left?.getRight()); // true

How to determine if one body part is contained by another?

To determine if a one body part is contained by another, use the isContained function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID56');
const bodyPart2 = index.get('RID199');
const isContained = bodyPart2?.isContained(bodyPart1);

How to get the contained children of a body part?

To get the immediate contained children, use the getImmediateContainedChildren function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID39569');
const immediateChildren = bodyPart1?.getImmediateContainedChildren();

To get all the contained children, use the getAllContainedChildren function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID39569');
const children = bodyPart1?.getAllContainedChildren();

How to get the contained ancestors of a body part?

To get the contained ancestors of a body part, use the getAllContainedAncestors function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID480');
const ancestors = bodyPart1?.getAllContainedAncestors();

How to determine if one body part is part of another?

To determine if a one body part is part of another, use the isPartOf function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID480');
const bodyPart2 = index.get('RID905');
const isPartOf = bodyPart2?.isPartOf(bodyPart1);

How to get the partOf children of a body part?

To get the immediate partOf children, use the getImmediatePartOfChildren function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID480');
const immediateChildren = bodyPart1?.getImmediatePartOfChildren();

To get all the partOf children, use the getAllPartOfChildren function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID480');
const children = bodyPart1?.getAllPartOfChildren();

How to get the partOf ancestors of a body part?

To get the partOf ancestors of a body part, use the getAllPartOfAncestors function.

const index = new BodyPartIndex();
const bodyPart1 = index.get('RID579');
const ancestors = bodyPart1?.getAllPartOfAncestors();