The PhenoDE Portal provides detailed information on Phenome Data Elements (PhenoDEs) and their associated phenotype variables. PhenoDEs includes a total of 58,297 data elements from Phase I of the International Human Phenome Project (IHPP), covering 22 phenotype measurement platforms ranging from macro to micro scales. On the Home page, clicking the navigation bar (①) in the top right corner will direct users to the corresponding modules. To search for PhenoDEs, users can enter the coding ID, Term, abbreviation, or variable ID of the corresponding PhenoDEs in the search bar (②). Additionally, searches can be performed using features or qualifiers terms.

e.g., PDE045007225.1, Heart-Average Heart Rate (inlineVF), AHR (inlineVF), PDV045007225.1_00100, Optic disc thickness, brain, Electrocardiograph, mm.

By clicking PhenoDEs in the formula (③) on the homepage, users can access the Browser page to view all data elements. The Platforms section (④) displays the abbreviations of the 22 platforms along with the total number of PhenoDEs; hovering over shows the full platform names, and clicking the number below each platform abbreviation leads to all PhenoDE pages for that platform. Using the Phenotype Assembly Method, PhenoDEs have been categorized into three types of features and ten types of qualifiers. The homepages pie chart (⑤) and bar chart (⑥) respectively display the number of categories for features and qualifiers.

Enter a query in the search bar to view results, including basic information on PhenoDEs and their associated feature and qualifiers categories (①). On the left side of the results page, users can refine the search using Feature categories (②), Qualifiers categories (③), and Detection items (④). Multiple qualifiers can be selected to filter PhenoDEs containing all chosen qualifiers. Clicking Clear All (⑤) will reset all filters. Click History and Search Details (⑥) to view your search history and the corresponding number of results.

Clicking on the PhenoDE term (displayed in blue text) from the search results in the Browser page directs users to the PhenoDE detail page.

The Basic Information (①) and Phenotype Variables (②) sections provide details for each PhenoDE and the statistical distribution of the corresponding phenotype variables. For PhenoDEs with multiple phenotype variables, selecting a specific Variable ID displays the graph corresponding to that phenotype variable. Statistical distribution characteristics are not shown for molecular phenotypes, including Total RNA and small RNA, Proteome, Microbiome, Metabolome, and Cell platforms. Users can view the statistical characteristics of each phenotype variable individually or select two variables to display them on the same page .

Phenotype variables are categorized as quantitative or qualitative. For quantitative variables (③), the first row displays box plots and density plots, while the second row shows density plots and Q-Q plots for relevant distribution tests. For qualitative variables (④), bar charts are used to illustrate the proportion of each category.

The Phenotype Assembly Method in DE section provides detailed assembly information. Users can click on any feature or qualifier (displayed in blue) to access their respective detail pages. By selecting checkboxes and clicking Search Selected Features and Qualifiers, users can search for PhenoDEs sharing the same features or qualifiers. In the schematic tree diagram, colored sections represent distinct features and qualifiers of the PhenoDE, while gray sections indicate adjacent features or qualifiers defined in the controlled vocabularies.

The Similar PhenoDEs section displays PhenoDEs with the same features or qualifiers as those on the current page. Users can click on the PhenoDE Term to view the respective detail pages or scroll horizontally to see the assembly information for similar PhenoDEs.

On the PhenoDE detail page, under the Phenotype Assembly Method in DE section, users can click to access the detail page for each feature. This page displays the basic information of the feature and its mapping information to data specifications (①). “Mapping result” is categorized as exact, partial, or unique, where unique indicates features that might not align with any existing data specifications. “Source type” refers to the data specifications involved in the mapping, including ontology, database, dataset, and literature. “Description” provides information on the platforms within IHPP that use this feature. “Link or ID” provides information such as ID within databases or DOI. Link or ID for ontology sources are predominantly derived from ID in BioPortal (https://bioportal.bioontology.org/). For features mapped from multiple sources, users can click the blue arrow to expand the information in Link or ID. The section PhenoDEs share this feature (②) displays the PhenoDEs that include this feature and its distribution across different platforms. Only 10 PhenoDEs are shown in the table; clicking More (③) allows users to view all PhenoDEs that utilize this feature.

On the PhenoDE detail page, under the Phenotype Assembly Method in DE section, users can click to access the detail page for each qualifier. This page follows a similar structure to the feature page and displays the basic information of the qualifier along with its mapping to data specifications (①). “Mapping result” is categorized as exact, partial, or unique, where unique indicates qualifiers that might not align with any existing data specifications. “Source type” refers to the data specifications involved in the mapping, including ontology and literature sources. “Description” provides information on the platforms within IHPP that use this qualifier. “Link or ID” provides identifiers such as IDs within BioPortal or DOIs. For qualifiers mapped from multiple sources, users can click the blue arrow to expand the Link or ID information. For the Qualifier Measurement Tool (MT), no mapping has been performed, so only basic information is displayed. The section PhenoDEs share this qualifier (②) shows the PhenoDEs that include this qualifier and its distribution across different platforms. Only 10 PhenoDEs are shown in the table; clicking More (③) will display all PhenoDEs that use this qualifier.

The Downloads page provides a downloadable PDF of the latest version of the PhenoDEs.

The About page includes sections for Overview, Supplementary Tables, Acknowledgment, and Contact Us. Users can explore detailed information on the IHPP platforms, detection items, and the full names corresponding to abbreviations for features and qualifiers, as well as browse related web content.