Exploring CMPO

 

Searching CMPO in OLS

The Ontology Lookup Service (OLS) allows you to search for terms within and across a number of biomedical ontologies. We can use OLS to explore CMPO for concepts or terms that we are interested in.

First, select CMPO from the drop-down "Search Ontology" menu. Then begin typing in the Term Name box - you can input term names you already know, or use free text. The OLS search includes a partial search term function, so as soon as you start typing you will begin to see suggested terms. The image below shows a search in progress for the term "elongated".

Figure 3 OLS search for terms containing the word "elongated".

The approach described above is useful if you want to find the CMPO terms to describe an observed phenotype. If you leave the "Search Ontology" drop-down menu showing the default "search in all ontologies" option, you can run a query across all the ontologies supported by OLS. This can help you to discover other ontologies with shared or similar terms; this is useful if you are planning to combine a number of ontologies or if you are integrating different annotated datasets (mouse and human disease data, for example).

If you have a previously annotated dataset that includes CMPO identifiers - CMPO:000XXXX - then you can use the "Simple Term ID Search" option shown above. Running a query on "CMPO:0000316" will return the CMPO entry for "abnormal cell growth".

Browsing CMPO in OLS

We can also use OLS to browse the entire ontology, instead of individual terms, allowing us to navigate the ontology structure and see more granular phenotypes. To do this, select CMPO from the drop-down "Search Ontology" menu; then click the "Browse" button on the right. This will open a new page with a visualisation window where the entire ontology will appear in branch form. You can expand the ontology by clicking on the "+" icon to the left of a term; child terms will then be visible. You can click the "-" icon to collapse branches back.

Figure 4 Ontology branches down to "abnormal nucleus shape phenotype".

CMPO term metadata

Once you have located a CMPO term - using the "Search Ontology", "Simple Term ID Search" or the "CMPO Ontology Browser" options - you can learn more about the term by viewing the associated metadata. When using the "Search Ontology" or "Simple Term ID Search" functions a box containing the metadata will appear below the search box. This includes information on: the definiton of the term, the preferred name of the term, its broader synonyms, and links to PubMed where the phenotype was reported (if available).

Figure 5 Metadata information on the CMPO "mitotic delay phenotype" term

CMPO term hierarchy

CMPO also allows you to explore a term within the context of the entire ontology. By clicking on the "Browse" button next to the "Search Ontology" drop-down menu, you will be taken to the OLS Browser. On the right-hand side you will find a box that contains graphical representation of where the selected term sits in the ontology hierarchy and its relationships to neighbouring terms. In the example below "mitosis delayed phenotype" is a term at the base of the ontology tree with no child terms. If we were investigating "delayed process phenotype", then we would be able to browse terms both above and below our term of interest.

Figure 6 Term hierarchy for "mitosis delayed phenotype"