Navigating a MedGen Record

MedGen Documentation Pages

|Overview| Searching MedGen | Navigating MedGen records | MedGen Data Processing and Curation | FAQ | Definition Sources |

You can contact the MedGen team with any questions or suggestions.

Overview of a MedGen record

Records in MedGen are classified by UMLS with an appropriate semantic types For example, a record with semantic type "Disease" includes data from OMIM, Mondo, Orphanet, or GeneReviews. Different records may contain different or fewer sections based on semantic type, available mappings from authoritative sources, or other limitations in the available data. Sections on the MedGen Record: 1. Disease names and record identifiers
2. Mode of inheritance
3. Genes associated with the condition
4. Images related to the disease record
5. External Identifiers
6. Disease description (Definition)
7. Additional description
8. Clinical features/ Conditions with feature
9. Term hierarchy
10. Professional Guidelines
11. PubMed Articles: Suggested Reading and Clinical Queries

Figure 1: Navigating MedGen Records

NavigatingRecords

There is also a Navigation and Discovery panel on the right-hand side of page.

Disease Names and record identifiers

This section includes the name of the disease as well as exact synonyms for the disease. Identifiers and names from SNOMED CT (US) as well as names from OMIM, Orphanet, Mondo or MedGen curation display in this section. Not all MedGen records will include SNOMED CT names and identifiers. The identifiers for the record include the MedGen UID (unique identifier, used by NCBI Entrez indexing and search) and the assigned Concept ID (CUI) from UMLS (formatted as C#######) or MedGen (formatted as CN#######). The semantic type for the term is also listed immediately underneath the preferred disease name.

Semantic types from UMLS

The UMLS Semantic Network classifies all UMLS terms and CUIs into a structured system to provide broad categories of concepts. Not all UMLS concepts are in scope for MedGen, however a CUI of an "out of scope" semantic type may be used to map terms from HPO. Over 99.4% of MedGen’s records with a UMLS CUI fall into the following categories:

MedGen diseases:

• Disease or Syndrome
• Neoplastic Process
• Pathologic Function
• Congenital Abnormality
• Anatomical Abnormality
• Cell or Molecular Dysfunction
• Mental or Behavioral Dysfunction

MedGen phenotypes:

• Finding
• Sign or Symptom
• Laboratory or Test Result

Mode of Inheritance

The mode of inheritance will be listed if one is provided by Orphanet for the record. Not all disease records include a Mode of Inheritance because our sources have not provided it. You can click on the hyperlinked text here to view the provided definition of the mode of inheritance.

Associated Genes

This section lists the human genes that are reported by OMIM or GeneReviews to be associated with the disease. The data in Genes (locations) is limited to gene(s) directly associated with this condition or phenotype; the location provided in parentheses is the chromosome, arm and chromosomal band where the gene is located.

The related genes section lists gene(s) associated with related conditions. For conditions in a hierarchy, the parent condition will list the genes associated with the children conditions. Gene symbols and cytogenetic locations are displayed from data reported by NCBI Gene. Gene relationships to the diseases in MedGen are drawn primarily from OMIM and GeneReviews. MedGen also curates gene to drug-response phenotypes based on FDA approved drug labeling and expert guidelines for pharmacogenetic implementation.

Images on MedGen records

This section of the record can include images from Elements of Morphology that are mapped based on HPO terms and curatorial review as well as images from an associated GeneReviews chapter. Not all MedGen records will have images in this section.

External Identifiers

The exact matching record identifiers from MedGen’s external sources are listed here. This can include Monarch Initiative’s Mondo ID, OMIM, OMIM Phenotypic series, Orphanet, or HPO. Please note that additional identifiers are included in the XML view of the MedGen record including MeSH and NCI codes but are not listed in this section on the web display.

Disease description and Additional description

MedGen aims to provide at least one definition or disease description/characteristics text from our authoritative sources. When available, a summary from GeneReviews is our preferred description. See our list of definition sources for additional details on other sources for this and the Additional Description field. When more than one source is available for a disease definition or description, MedGen provides the additional data in the "Additional description" section.

Clinical features

Phenotype terms from HPO that have been annotated by HPO are included in this section of disease records. Associated phenotypes, or clinical features, are grouped according to HPO’s terminology. Clicking the arrow next to one of the terms will show the specific phenotypes under that category, or you can click "show all" to see all the specific phenotypes. The "Hide all" link will collapse all HPO categories as well; the show and hide all options will be available only if there are multiple HPO categories to expand or collapse. If you click on one of the specific phenotypes, it will open a window that shows the MedGen UID, CUI, and Semantic type as well as HPO’s definition for that phenotype. There are also links to view that phenotype record in MedGen or search MedGen for that clinical feature. (Note that this search can also be run from the phenotype entry in MedGen.

Figure 2: Clinical Features Pop-up
Clincal Features

Phenotype entries in MedGen have a unique section: Conditions with this feature {#condwithfeat}. This section lists all diseases in MedGen that have been annotated in HPO to have this clinical feature. If more than 5 disease entities contain the feature, there will be an option to "See full list" with a count in parentheses of the number of matching conditions.

Figure 3: Conditions with this feature
ConditionsWithFeature

Rarely, a condition from OMIM and a clinical feature from HPO may map to the same UMLS CUI, in this case both the Clinical Features and Conditions with this Feature sections will be present to help find other disorders with the same single feature or capture other clinical features that define the OMIM related disease.

Term Hierarchy

This section can include MedGen’s curated disease hierarchical relationships (GTR tab), MeSH hierarchy (MeSH), or a link to Orphanet’s hierarchy of disease records (Orphanet). On the GTR tab, there is also a summary of what mappings or associated data exist for the primary record as well as the other terms in the hierarchy (C- clinical test in GTR, R- research test in GTR, O- data from OMIM, G- GeneReviews associated information, V- Variant submitted to ClinVar). Clicking on a disease name in the hierarchy table will navigate to that MedGen entry.

Figure 4: Term Hierarchy
Hierarchy

Professional practice guidelines

MedGen offers a detailed PubMed-based search pre-built for clinicians to find disease-specific practice guidelines. On each condition page, you will find the top results from our custom query of PubMed articles that has been specifically tailored to capture a wide range of practice guidelines for that condition. Additionally, there is a link to see the full search results in PubMed. If the PubMed search does not return any articles, we provide a search for a related broader concept to assist you in finding the most relevant information. For additional details on these queries please see our FAQ on Professional Practice Guidelines. There is also subsection for Curated Practice guidelines. The team of Medical Genetics Curators at NCBI have identified professional and medical societies that issue practice guidelines which are not included in PubMed or Bookshelf. These are added manually to display under the section "Curated Practice Guidelines". If there are specific practice guidelines that are not listed in this section, you can help us improve MedGen by reporting them to us at medgen_help@ncbi.nlm.nih.gov.

Suggested Reading and Clinical PubMed searches

Suggested Reading: This optional section may display when MedGen expert curators have identified a publication that is highly relevant or important for the MedGen record and want to ensure it is discoverable by our users. Recent clinical studies This section (Figure 5) is generated at the time of display of the web page. It uses the title of the record as a query and processes that title as if it had been submitted as a clinical query to PubMed (PubMed Clinical Queries), with display of the results in the Clinical Study Categories section, selecting Diagnosis with broad scope. Additional filters are applied, namely English language and human, and not comment publication types nor letter publication types. The results are presented in 5 subsections of Etiology (B), Diagnosis (C), Therapy (D), Prognosis (E), and Clinical prediction guides (F).

Figure 5: Names and Identifiers
Names and Identifiers

Recent systematic reviews

This section (Figure 5- G) is generated at the time of display of the web page. It uses the title of the record as a query and processes that title as if it had been submitted as a clinical query to PubMed (PubMed Clinical Queries), with display of the results in the Systemic Reviews section. Additional filters are applied, namely English language and human, and not comment publication types nor letter publication types.

Discovery panel at the right

The right-hand section of all MedGen pages contains a table of contents for the page and various sections of links to additional resources from National Library of Medicine or external resources that MedGen has identified as potentially relevant resources.

Figure 6: Navigation Bar
NavigationBar

Table of contents and page navigation

The table of contents summarizes the sections that are available in the record being displayed. Each term is hyperlinked to support quick navigation to that section. When you are within the page, the Go to link at the top of any section header provides a pull-down menu with quick links to other sections.

Figure 7: Section header navigation bar
NavigationSectionHeader

NIH Genetic Testing Registry (GTR)

The NIH Genetic Testing Registry section lists the types of genetic tests that are reported in the GTR for the condition or phenotype, according to the primary method being used. The section provides links to all tests, or tests using the method category being listed. This section will not display if there are no tests in GTR linked to the record in MedGen.

Figure 8: Navigation to GTR Tests
NavigationBar_GTRLinks

Clinical Resources

Additional resources with an emphasis on clinical use or practice are included in this section. This can include links to OMIM and Orphanet descriptions or a link to search ClinicalTrials.gov using the MedGen preferred name. Pharmacologic response terms should also include a link to PharmGKB’s entry for the drug.

Practice guidelines

Links to search PubMed and NCBI Bookshelf with MedGen developed queries are provided in this section. If there is a curated practice guideline(s) with the record, these will be listed in the "Curated" subsection of the Practice Guidelines section as well. The curated guidelines are displayed with the abbreviation of the issuing organization and year the guideline was issued. For additional details on Practice Guidelines please see our FAQ on Professional Practice Guidelines.

Consumer Resources

This section provides links to resources that may be more useful to the general public or non-clinical users of MedGen. These resources can include MalaCards, MedlinePlus and MedlinePlus Genetics, as well as the Genetics and Rare Disease (GARD) information center.

Reviews

This section provides quick links to search PubMed using either Clinical Queries or any publication flagged as a Review in PubMed. The Clinical Queries link will open a page with the MedGen preferred name prepopulated in the search box for the Clinical Queries interface of PubMed.

Related information

This section includes links to various NCBI and NLM-housed resources and projects to enable discovery and research. Linked projects include ClinVar, GTR, MeSH, NCBI Bookshelf, OMIM at NCBI, PubMedCentral articles (free full text articles housed at NCBI), PubMed and PubMed links based on cited articles from OMIM.

Recent history

At the bottom of nearly all NCBI pages you will find a list of recent searches and pages viewed from NCBI resources. You have the option to turn off this history recording or clear your session history here. You can also See more results if needed to find a previously viewed page or tab.

Alternate record views

Summary (Text)

This view provides a brief summary including the record Title, a Definition, the record Semantic Type, the Semantic ID (from UMLS), Concept ID (CUI, either UMLS or NCBI provided), ID (Entrez’s MedGen UID).

Summary (XML)

This full document summary in structured format includes the date and time-stamp for the most recent database build (DbBuild), Concept ID (CUI), Title, Definition, Semantic Id and Type. The Concept Metadata section includes names and the values from UMLS and MedGen such as the source ID and codes, source vocabulary (SAB), term type (TTY) and what type of name it is. The Definition and definition source, modes of inheritance, whether the term is a pharmacologic response, OMIM or other source identifiers. If clinical features are mapped to the record, they will be listed with the MedGen UID, CUI, source unique identifier (i.e. HPO Identifier), name, semantic type and definition for each feature. Clinical features may also be grouped into Categories by HPO; the CUI and Name for each category are provided. Additional information included in the XML are Related Disorders, SNOMED CT codes, and Associated Genes along with the NCBI Gene ID, chromosome and cytogenetic location and gene symbol for each.

Last updated: March 2025