Data that the National Library of Medicine maintains for the Newborn Screening Codes Web site are available in an XML file. The file is current with the data "views" also on the Web site.
This document complements the data file's formal XML schema.
The data file contains three kinds of entities:
The data file also associates conditions and measurements with standard clinical medical terminologies, controlled vocabularies, and other online databases or resources (see Referenced terminologies and databases below). These associations can facilitate joining information from other sources that also are indexed to the same well-known vocabularies or databases.
In order to associate markers with conditions and analytes, the data file tags each condition and analyte with an "xml-file-key". Markers refer back to those keys. The "xml-file-keys" do not have any significance outside this file.
We intend to keep the "xml-file-keys" stable over time (even as the names of things might change) to facilitate comparison of successive versions of the data file.
The document element, <newborn-screening-codes>, has the following properties. (For precise XML-element or XML-attribute characteristics, see the XML Schema.)
| Property | Notes |
|---|---|
| last-updated-date | The Newborn Screening Codes Web site "last updated" date. |
| version | File format. This document describes format "1.0". The version number corresponds to the structure, not the contents, of the file. |
The document properties are followed by three lists:
The following sections describe those lists.
The condition list is a collection of <condition> elements, in stable order by the "xml-file-key" property. Each condition record includes properties and terminology references.
The table below enumerates the property elements within <condition>. The "Notes" explain properties that do not closely correspond to fields explained on the Newborn Screening Codes Web site.
| Property | Notes |
|---|---|
| xml-file-key | Identifier for the condition within this file. |
| created-date | When the record joined the Newborn Screening Codes database. |
| modified-date | When the record was last modified in the Newborn Screening Codes database. Missing if the record has not been modified. |
| page | The URL for the condition on the Newborn Screening Codes Web site. |
| name | Condition name. |
| abbreviation | A short name. |
| affected-protein-memo | The structure that is abnormal, if xrefs provide no EC# or UniProt number. |
| description | A definition or description. The contents are XHTML. |
Newborn Screening Codes links each condition with various databases and vocabularies by means of a collection of <xref> elements. The same uniform <xref> structure accommodates references of all kinds. The set of referenced resources may grow in the future without a change to the file format.
Each <xref> element associates the condition with an entry in a vocabulary, database, or other resource. The following table shows how the <xref> properties make reference to each database.
In general, the "db" property indicates the resource, the "dbkey" property holds the primary key value appropriate for the resource (documented in the table below), and the "memo" property is a term or mnemonic that corresponds to the key value.
For some databases (marked with * in the Quantity column), the file provides a positive indication of the lack of an association. In this case, the <xref> has no dbkey, and a memo of either "N/A" or "None". "N/A" indicates that the topic is beyond the scope of the database; "None" indicates that the resource does not have a suitable code for the topic.
| Vocabulary, Database, or Resource | Quantity per Condition | <xref> property | ||
|---|---|---|---|---|
| db | dbkey | memo | ||
| IntEnz (Enzyme Commission) | 1* | enzyme-code | EC# | Recommended name |
| Genetics Home Reference | 0+ | ghr | URL | Summary title |
| ICD-9-CM | 1* | icd9cm | ICD-9-CM code | Preferred term |
| ICD-10-CM | 1* | icd10cm | ICD-10-CM code | Preferred term |
| OMIM | 1+ * | mim | MIM number | Entry title |
| Recommended Uniform Screening Panel | 1 | sachdnc-cat | "Core", "Secondary", or "Other" (not part of the Recommended Uniform Screening Panel) | |
| SNOMED CT | 1* | snomed-ct | SNOMED code | Preferred term |
| UMLS | 1* | umls-cui | CUI | (<memo> omitted) |
| UniProt | 1+ * | uniprot | Accession number | Recommended name |
The measurement list is a collection of <measurement> elements, in stable order by the "xml-file-key" property. Each measurement record includes properties and terminology references.
| Property | Notes |
|---|---|
| xml-file-key | Identifier for the measurement within this file. |
| created-date | When the record joined the Newborn Screening Codes database. |
| modified-date | When the record was last modified in the Newborn Screening Codes database. |
| page | The URL for the measurement on the Newborn Screening Codes Web site. |
| name | Analyte name. |
| short-name | A short name for the analyte. |
| units | What is being counted or measured. |
| Vocabulary, Database, or Resource | Quantity per Measurement | <xref> property | ||
|---|---|---|---|---|
| db | dbkey | memo | ||
| LOINC | 0-1 | loinc | LOINC_NUM | Long Common Name |
The marker list is a collection of <marker> elements, in stable order by condition-xml-file-key and measurement-xml-file-key.
Each <marker> is the association of a condition with a measurement. The marker list corresponds to the Newborn Screening Codes Web site reports of "Conditions and the Analytes/Measurements that serve as markers" and "Analytes/Measurements and the Conditions they signal".
| Property | Notes |
|---|---|
| condition-xml-file-key | Reference to a condition in this file. |
| measurement-xml-file-key | Reference to a measurement in this file. |
The addition or removal of a marker relationship is reflected in the modified-date of the affected condition and measurement.
These databases are the targets of "xref" elements in the Newborn Screening Codes data file. The data file contains only a code and a name for each reference. Complete records are available from the respective database, under its terms of use.
