Vyasa-Supported Ontologies

A list of all ontologies currently available off-the-shelf in Vyasa products.

Table of Available Ontologies

OntologyAcronymAuthorVersionLast Updated
Current Procedural TerminologyCPTAmerican Medical Association (AMA)2020AB01/06/2021
Experimental Factor OntologyEFOEMBL’s European Bioinformatics Institute (EMBL-EBI)3.39.102/24/2022
Foundational Model of AnatomyFMANIH NLM’s Unified Medical Language System (UMLS)5.0.005/13/2019
Gene OntologyGOGO Consortium2022-01-1301/18/2022
Human Phenotype OntologyHPOMonarch Initiative2022-02-1402/14/2022
International Classification of Diseases, Version 9 – Clinical ModificationICD-9 CMNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
International Classification of Diseases, Version 10ICD-10NIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
International Classification of Diseases, Version 10 – Clinical ModificationICD-10 CMNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
International Classification of Diseases, Version 10 – Procedure Coding SystemICD-10 PCSNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
Logical Observation Identifier Names and CodesLOINCNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
Medical Dictionary for Regulatory Activities TerminologyMedDRAMedDRA MSSO2021AB11/18/2021
Medical Subject HeadingsMeSHNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
National Cancer Institute ThesaurusNCITNIH’s National Cancer Institute (NCI)22.02d03/01/2022
Ontology of Consumer Health VocabularyOCHVAmith et. al (2019)Version 1.009/25/2019
Online Mendelian Inheritance in ManOMIMNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
Orphanet Rare Disease OntologyORDOFrench National Institute for Health and Medical Research (INSERM)Version 4.012/15/2021
PLOS ThesaurusPLOSTHESPLOS Taxonomy Team2017-1 (BioPortal)
2020-1 (GitHub)
09/21/2017 (BioPortal)
RxNORMRxNORMNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
Systematized Nomenclature of Medicine, International VersionSNMI (SNOMED)NIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
Systematized Nomenclature of Medicine, Clinical TermsSNOMED CTNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021
World Health Organization (WHO) Adverse Reaction TerminologyWHO-ARTNIH NLM’s Unified Medical Language System (UMLS)2021AB11/18/2021

Interested in adding one or several of these ontologies to your instances? Reach out to [email protected] or someone on our support team for assistance.

Load Table-Based Ontologies into Layar

A quick guide on how to upload your own ontologies into Vyasa Layar for implementation.

Table-Based Files (.csv, .xls, etc)

Step 1. Add your ontology file to Layar using one of your connectors (or local upload).

  • The ontology file can be any table-based file (for example, .csv, .tsv, .xls, etc are all compatible).
  • The system currently does not detect multiple sheets within your file. If you have multiple tabs of tables within your file, please save each sheet as a separate file before uploading to Layar.

Step 2. Once uploaded, click the file of interest within Layar.

Step 3. Click the vertical three-dot icon on any of the column headers within the table.

Step 4. Select “Create Ontology“.

Step 5. Give your ontology a name, and identify which column will populate the following properties:

  • Label (Required): The column you assign to this property will be considered the preferred label. These are the labels you will see when you view and navigate your ontology in the Ontologies section of Layar.
  • Synonyms: You can assign multiple columns to this property. All columns assigned to the synonyms property will be displayed as synonyms for a term. This synonym property is further used when running an explosive search in Layar. For example, the term “Tachycardia” has 48 synonyms for different uploaded ontologies uploaded to Layar, which you can expand your search to include.

Note: If any of your columns list out multiple synonyms as a list, identify what delimiter should be used to separate each term out as an independent synonym.For example: The list “Heart attack | Acute cardiac arrest | cardiac myopathy”, which are synonyms for “Heart Attack”, is pipe (|) delimited.

  • ID: If there is an ID or code associated with a label (such as the medical codes associated with a term in the ICD-10). These are specific to the ontology, and you can only select one.
  • Parents/Path/Superclass/SubClassOf: If your ontology is hierarchical, identify which column identifies the relation. You can only select one column. The column must refer to the “parent” term, also known as the class that term belongs to (e.g., “Cardiovascular Diseases” is the parent of “Heart Attack”).
  • Other Properties: Any other properties you wish to have connected to a term from the original table will be populated here. You can modify the list of other properties to your liking, and each property added into the “Other Properties” field will be treated as their own independent properties within the created ontology.
  • Delimiter: Finally, if any of the columns selected for the above properties uses delimiters to define a list in a cell, define that delimiter here. We typically suggest not using a comma (,) or hyphen (-) delimiter in your ontologies, as those are regularly used in nomenclature as part of your term (e.g., caffeine is also known as “1,3,7-Trimethylpurine-2,6-dione”. If you assigned a comma delimiter, you’d get synonyms “1”, “3”, 7-Trimethylpurine-2″, etc.
    Example delimiters:

Step 6. Once you are satisfied with the properties you’ve assigned, click “Create Ontology”.

Step 7. Your table will now be converted to into an ontology, which you can view by going to your “Ontologies” tab in the left-hand menu, and clicking on the name of your ontology.

Note: If your ontology is larger than 300 MB, or is hierarchical in nature, you may need to wait a few minutes before being able to view the classes in your ontology. You do not have to wait for this process- you can click out of the “Create Ontology from Table” popup and work on other things in Layar while the ontology is generated behind the scenes.

If you are creating an ontology from an .obo or .owl file, please read the following documentation.

To edit and modify ontologies further, see “How to Edit Ontologies“. This article will provide you with more information on the different capabilities available in Layar for you to edit your ontology.