EarthPortal provides different tools to access, use and manage semantic artefacts including:
- browse the semantic artefacts;
- search for a term across multiple semantic artefacts;
- browse mappings among terms in different semantic artefacts;
- receive recommendations on which semantic artefacts are most relevant for a given corpus;
- annotate text with terms from semantic artefacts;
All information available through the EarthPortal website is also available through the REST API documentation.
Browse
The Browse tool allows users to search for semantic artefacts. When opening the browser page (Figure 3), there are two options:
- scroll the full list of semantic artefacts and select one to see more detailed information (Browse all);
- type the semantic artefact name or abbreviation in the Search bar.
Figure 3: Browser page
In both cases, the search can be further refined by using the filters provided on the left side of the page (Show semantic resource views, Show retired semantic resources, Categories, Groups, Natural languages, Formality levels, Semantic resource types). Upon selecting the filter, the search will be updated to show results which contain the selected filter. Repeat the process to add additional filters.
Moreover, using the tabs on the right side of the search bar, the list of semantic artefacts can be sorted by choosing the type of format (SKOS, OWL, UMLS, OBO) or other desired criteria:
- Name: alphabetical order;
- Classes count: number of classes;
- Instances/concepts count: number of instances or concepts;
- Submitted date: date of last submission;
- Creation date: date of publication;
- FAIR score: O’FAIRe tool score;
- Popularity: number of visits to the semantic artefact;
- Notes: number of notes issued for the semantic artefacts;
- Projects: number of projects where semantic artefacts are used.
To access semantic artefacts through the API, see our Resources REST API documentation.
In the browse page, the “Submit new semantic artefact” button is also available on the upper-left part of the page, but users need to be logged in to perform this operation.
For more information about publishing a new semantic artefact in EcoPortal, please visit the guide.
- Popular: number of visits to the semantic artefact;
- Name: alphabetical order;
- Class count: number of classes or concepts;
- Instances/concepts count: number of instances or concepts;
- Projects: number of projects where the semantic artefact is used;
- Notes: number of notes issued for that semantic artefact;
- Upload Date: date of last submission;
- Release Date: date of publication;
To access semantic artefacts programmatically, see our Resources REST API documentation. In the browse page, the “Submit New semantic artefact” button is also available on the upper-left part of the page, but users need to be logged in to perform this operation. For more information about publishing a new semantic artefact in EarthPortal, please visit the guide.
Search
The Search option allows users to find a term across semantic artefacts by clicking on the arrow pointing to the right in the home page search box and entering free text in the “Enter a term” bar. The system looks for matches in the term name, synonyms, term IDs, and in property values.
The advanced search options can be used to add (Figure 4):
- Property values: named association between two entities. Examples are “definition” (a relationship between a class and some text) and “part of” (a relationship between two classes).
- Obsolete classes: a class that the authors of the semantic artefact have flagged as being obsolete. These classes are often left in semantic artefacts so that existing systems that depend on them will continue to function.
- Semantic resource views: search only ontological views.
Users can also narrow the search by selecting “exact matches” and/or “classes with definitions” or by selecting one or more categories and/or semantic artefacts using the “Categories” and “Semantic resources” fields. In addition, it is possible to perform a broader search by selecting one or more federated OntoPortal instances, namely AgroPortal, BiodivPortal and EarthPortal, from the section “Results from external portals”.
Figure 4: The search tool
To allow better performances, the search result is limited to the top 100 matches.
The search result within EcoPortal will display the matched terms and their associated semantic artefact. For each search result it is also shown:
- details: a window with the associated properties of the searched term;
- visualize: the graph with the nodes of the terms and the path to the root;
- <_number_> _more from this semantic resource_: other similar terms within the semantic artefact are shown.
If a federated search is performed, for each search result it is shown:
- <_number_> _more from this semantic resource_;
- the badge of the OntoPortal instance in which the result can be found.
Search can be done using the API directly. To learn more, see our Search REST API documentation.
Annotator
The Annotator tool enables the generation of annotations by entering or pasting free text in the box and clicking on the “Get Annotations” button (Figure 5).
The system matches words in the text to terms from the semantic artefacts available in the portal by doing an exact string comparison (a “direct” match) between the text and names, synonyms, and IDs of terms within the semantic artefacts. The set of matches can be expanded by including matches from mapped terms and from hierarchical expansion. The system performs the hierarchical expansion on the superclass (“is-a”) relationship for most semantic artefacts, including OWL and UMLS RFF. For OBO semantic artefacts the hierarchical expansion also includes the “part-of” relationship. The “number of levels” can be used to control the number of levels up the hierarchy for which the system will return terms for a given match. For more details about the Annotator tool, please read Shah et al., 2009. To generate annotations from the API, see the REST API documentation.
Figure 5: The annotator tool