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Pierfrancesco Tommasino edited this page Apr 19, 2021 · 102 revisions

Home Page

The EcoPortal Home Page is constituted by:

  • a header that includes the logo on the left and the navigation bar to the right;
  • two calls to actions and some statistical information as plain content;
  • a footer that includes all the support information.

EcoPortal

  • NavBar Ecoportal
    The navigation bar on the upper right side of the web page includes 4 menu items to navigate within EcoPortal:
    1. Login - to access the login/registration form. If you are already logged in, your username will be displayed here.
    2. Tools - to access the list of tools provided by EcoPortal, that are:
    3. Support - to ask for support in relation to questions, error reports, feedback, etc. by means of a user-friendly contact form.
    4. About Us - information in relation to who we are, what LifeWatch ERIC is and what EcoPortal is.

The Home Page contains two sections where you can quickly view or query the available resources. In particular:

  • you can quickly search for terms by entering a class name into the "Search for a class" field in the form to be redirected to the page showing the results;
  • you can start entering free text in the "Find a semantic resource" field in order to quickly find the resource you are interested in by using the autocompletion functionality and then selecting the summary page.

Moreover, you can also see the EcoPortal statistics such as number of published resources, number of classes, etc.

  • Footer
    The footer includes all EcoPortal support links, divided into 4 sections:
    1. Products:
    2. Support:
      • Contact Us: to ask for support in relation to questions, error reports, feedback, etc. by means of a user-friendly contact form
      • Help: to access information on how to get started and how to find documentation
      • EcoPortal Wiki Documentation: to access this online documentation.
    3. About:
      • About us: to read information in relation to who we are, what LifeWatch ERIC is and what EcoPortal is.
      • Team: to see the EcoPortal team members
      • Project: to view selected projects which make use of EcoPortal resources. To add your project to this list, click the "Create New Project" button. You must be logged into EcoPortal to create a new project.
    4. Connect - shortcuts to access our social media channels.

EcoPortal provides access to ecological semantic resources and tools for working with them. EcoPortal allows you to:

All information available through the EcoPortal website is also available through the EcoPortal Web service REST API. Please see REST API documentation for more information.

  • Login EcoPortal

    Login EcoPortal: link

  • Registration EcoPortal

    Registration EcoPortal: link

Tools

  • Browse

    The Browser tool allows you to search semantic resources. When you open the browser page to find a semantic resource, you have two options:

    1. you can go through the list and select the semantic resource to see more detailed information;
    2. you can start typing the semantic resource name or abbreviation in the “Search…” field.

    Browse page screen

    In both cases, you can further refine your search by using the filters provided on the left-hand side of the page. To add a filter to your search, click the checkbox or filter label. 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, you can sort the list by choosing the desired criteria (upper right side of the list of resource):

    • Popular: number of visits to the semantic resource
    • Size: number of classes or concepts
    • Projects: number of projects where the semantic resource is used
    • Notes: number of notes issued for that semantic resource
    • Upload Date: date of last submission

    Furthermore, once logged into EcoPortal, in the "Account Settings" section, you can select only the semantic resources that you need to see without viewing others.

    Custom semantic resource set: in Settings Page Account

    To access semantic resources programmatically, see our Resources REST API documentation (then take a look under Media Types). You will be able to see semantic resources that are marked “Public” because submitters have the facility to control who can browse the terms in their semantic resources by marking them with “Public” or “Private” visibility. In order to browse the terms in these private resources you have to be logged into EcoPortal and have access to the semantic resource. In particular:

    • for public semantic resource, the resources are accessible and can be viewed by all users even if they are not logged in;
    • for private semantic resources, the submitter directly controls the access. In order to gain access to a specific private semantic resource you have to contact the submitter and you must be registered in EcoPortal. Private semantic resources will not be indexed in the search.

    In the same browser page, you will find the “Publish New Semantic Resource” button on the upper-left part of the page, but you need to be logged in to EcoPortal to perform this operation. Once you click the button, you have to select the required fields (marked with a red *) as described in ”How to publish a semantic resource”.

    Once opened the selected semantic resource, the summary page will show the different areas:

    1. menu area
    2. details area
    3. download area
    4. metrics area
    5. submission area
    6. views area
    7. project area

    Summary page semantic resource

    • Menu Area

      The menu area allows you to:

      • View classes
      • View properties
      • View and edit notes
      • View and edit mappings
      • Select a widget

      Classes

      Classes Page

      In the summary page of the semantic resource, when clicking on Tab Classes, you will see:

      • on the top of the left column a search field for classes and concepts discovery; below the navigation tree of the concepts or interactive classes, whether it is ontology or controlled vocabulary;
      • on the right column an area with Details, Visualization, Notes and Mappings related to the selected class/concept:

        • Details: tab showing properties and relationships associated with the selected class/concept. The properties shown will differ according to the representation model of the resource (SKOS; OWL, UMLS; OBO). The custom properties are also displayed, for example: ID, created, definition, etc.

        • Visualization: EcoPortal displays semantic resources as a graph in which the resource concepts are represented by nodes and the relationships among concepts are displayed as edges among the nodes. By default, the most basic directional relationships (parent/child relationships) are identified by a solid navy-blue line with an arrow pointing to the child concept. Mappings are identified by a solid light-grey line. However, depending on the construction of your semantic resource, EcoPortal can display other types of relationships.

          Visualization Page

        • Notes: tab showing all the notes issued by EcoPortal users in relation to the selected class/concept. You must be logged in to be able to issue generic comments or proposals regarding new classes, new relationships or to change properties.

        • Class Mappings: tab showing all the mappings associated with the selected class/concept. For each mapping you can see:

          • mapping to: the name of the selected class/concept mapped to the class/concept of another resource;
          • semantic resource: the semantic resource of the mapped class/concept;
          • source: the mapping algorithm.
            Mappings with source equal to LOOM are automatically identified by EcoPortal. Furthermore, you can click on the "Create new Mapping" button to manually insert mappings by filling in the following fields: target semantic resource or view; target class; details; comment; mapping relation type.

          Class Mappings Page

      Properties
      In the summary page of the selected semantic resource, when clicking on Properties Tab, you can see all the properties used within the selected semantic resource. The same as for the Classes Tab, the interactive property tree is shown on the left, while the property details are shown on the right.

      Property details Page

      Notes
      In the Notes tab you can see all the comments or proposals issued by registered EcoPortal users. You can add comments or proposals only if you are registered and logged in by clicking on the "Add Comment" and "Add Proposal" buttons.

      Notes section details Page

      • Add a new comment: you can send a comment to the owner of the resource by specifying the subject and writing a free text comment.
        Add new comment form
      • Add a new proposal: you can send a proposal to the owner of the resource to modify or create new relationships or classes/concepts.
        Add new proposal form
      • Subscribe/Unsubscribe to notes emails: you can subscribe to receive emails whenever comments or proposals from other users are provided by clicking on the "Subscribe to notes emails" link. You can manage your subscriptions on the “Account Settings” page and click on “Unsubscribe” link to stop receiving emails.

      Mappings
      In the Mappings Tab you can see all the mappings of the selected semantic resource. The table includes two columns: Semantic Resource and Mappings. The first identifies the semantic resource where mappings are found, and the second shows the number of mappings. You can click on a semantic resource to see all the mappings found.

      Mappings Page Resource

      Widgets
      In the Widgets Tab you can see different types of widgets that you can use within a web page. The types of widgets available within EcoPortal are:

      • Jump To: type a class in the selected semantic resource and jump to it in EcoPortal;
      • Form Autocomplete: fill in a field in your form with a class from the selected semantic resource;
      • Visualization: display a visualization for a given class/concept in the selected semantic resource;
      • Tree Widget: display a tree for classes in the selected semantic resource with a search field. You can use the widgets only if you are registered in EcoPortal with an associated API-KEY.

      Widgets page

    • Details Area

      In the detail area you can view the EcoPortal metadata schema present for the selected semantic resource. The metadata reported under the Details heading are taken from metadata schema provided by BioPortal:

      ACRONYM The semantic resource acronym
      VISIBILITY Resource visibility: Private or Public. You will only be able to read Private resources if you have previously requested access to them.
      DESCRIPTION Description of the resource
      STATUS Resource release status: alpha, pre-production. production, etc.
      FORMAT Resource format: SKOS,OWL,UMLS,OBO
      CONTACT Contact information for the resource authors
      HOME PAGE The homepage for the resource:URL
      PUBLICATIONS PAGE Resource publication page:URL
      DOCUMENTATION PAGE Resource documentation page:URL
      CATEGORIES Categories to which the resource belongs
      GROUPS Groups to which the resource belongs

      In the Additional Metadata section, instead, you will find the DataCite Metadata Schema v4.3 needed to obtain the DOI (Digital Object Identifier):

      IDENTIFIER The DOI (Digital Object Identifier) or other identifier (e.g., PID) of the resource if it exists with the format “10.1234/foo”.
      IDENTIFIER TYPE Controlled List Value: DOI, Other
      RELEASE DATE Date on which the resource was published / released on EcoPortal
      CREATORS The main researchers/institution/organization involved in producing the resource, in priority order. May be a corporate/institutional or personal name.
      TITLES A name or title by which a resource is known. The title is a controlled list of values: AlternativeTitle, Subtitle, TranslatedTitle, Other.
      PUBLISHER The name of the entity that holds, archives, publishes prints, distributes, releases, issues, or produces the resource. This property will be used to formulate the citation, so consider the prominence of the role. In EcoPortal, if a DOI is requested, the publisher will always be: LifeWatch ERIC.
      PUBLICATION YEAR The year when the data was or will be made publicly available.
      RESOURCE TYPE A description of the resource. E.g.: Controlled Vocabulary, Ontology.
      RESOURCE TYPE GENERAL The general type of a resource.

    • Download Area

      On the right side of the summary page and above the metrics area there are two buttons for downloading metadata:

      • Json (DATACITE) button provides the DataCite metadata;
      • Json (ECOPORTAL) button provides all EcoPortal metadata.

      DownloadArea

    • Metrics Area

      This section describes the metrics that EcoPortal calculates for the semantic resources in its repository. EcoPortal calculates metrics when the semantic resource is uploaded and will store them as part of the BioPortal Ontology Metadata. There are two groups of metrics:

      • statistical metrics;
      • quality-control and quality-assurance metrics.

      Some metrics are meaningful only for semantic resources in a specific representation language (e.g., there are no individuals to count in the ontologies in OBO format).

      Metrics Table

      Statistical Metrics are calculated on each semantic resource:

      • number of classes: the number of named (not anonymous) classes in the semantic resource;
      • number of individuals: the number of individuals in the semantic resource;
      • number of properties: the number of properties or slots in the semantic resource;
      • maximum depth: the maximum depth of the hierarchy tree:
        • for OWL, RDFS, Protege, and RRF ontologies, we consider only the "is-a" relationship as a hierarchical relationship;
        • for OBO format ontologies, we consider the following relationships as hierarchical relationships: "is-a", "has-part", "inverse" and "develops-from";
      • maximum number of children: the maximum number of children in the semantic resource;
      • average number of children: the average number of children at one level in the tree.

      Quality-Control and Quality-Assurance Metrics provide some indication of the quality of the semantic resource and help semantic resource authors to improve their quality. To improve their usefulness, we limit the size of lists for any one of these metrics to 200. Semantic resources with more than 200 classes in a category will still have the total number of classes in that category counted, but no list will be available. Please notice that:

      • classes with a single child: a list of classes that have only one subclass in the is-a hierarchy. While technically there is no problem in having only one subclass, this situation often indicates that either the hierarchy is under-specified, or the distinction between the class and the subclass is not appropriate;
      • classes with more than 25 children: a list of classes that have more than direct subclasses. A class that has more than 25 subclasses is a candidate for which additional distinctions and categorization are needed;
      • classes with no definition: a list of classes that have no value for the definition property. For ontologies in OBO and RRF formats, the property for definition is part of the language. For OWL ontologies, the authors specify this property as part of the ontology metadata (the default is "skos:definition").

      For more details about the metrics generation, please visit https://www.bioontology.org/wiki/Ontology_Metrics. EcoPortal users will be able to access semantic resource metrics in two ways:

      • through the EcoPortal user interface, in the metrics area of the summary page (see example here);
      • through a dedicated REST service that returns a JSON.

      In relation to the REST access, for example, the following REST service can be used:

      http://ecoportal.lifewatch.eu:8080/ontologies/FISHTRAITS/metrics?apikey=YourAPIKey

      The service returns a JSON that contains the version id for the semantic resource and the values for the metrics:

      {
"id": "http://193.204.79.110:8080/ontologies/FISHTRAITS/submissions/1/metrics",
"classes": 2,
"individuals": 220,
"created": "2019-05-27T07:00:40-07:00",
"properties": 0,
"maxDepth": 0,
"maxChildCount": 2,
"averageChildCount": 2,
"classesWithOneChild": 0,
"classesWithMoreThan25Children": 0,
"classesWithNoDefinition": 2,
"submission": [
       "http://193.204.79.110:8080/ontologies/FISHTRAITS/submissions/1"
],
"@id": "http://193.204.79.110:8080/ontologies/FISHTRAITS/submissions/1/metrics",
"@type": "http://data.bioontology.org/metadata/Metrics",
"links": {
       "ontology": "http://193.204.79.110:8080/ontologies/FISHTRAITS",
       "submission": "http://193.204.79.110:8080/ontologies/FISHTRAITS/submissions/1",
"@context": {
       "ontology": "http://data.bioontology.org/metadata/Ontology",
       "submission": "http://data.bioontology.org/metadata/OntologySubmission"
 }
},
"@context": {
       "@vocab": "http://data.bioontology.org/metadata/"
}
}

      If a given semantic resource has more than 200 classes identified for any single metric, then that metric will provide an error message in place of the class list. Two states are available:

      • limitpassed: it means that the 200-class limit was reached and passed. When this error presents, it is followed by the total number of classes in the semantic resource that matches this metric;
      • alltriggered: it means that every class in the semantic resource matched this metric.

    • Submission Area

      SubmissionArea

      In the submission area all submissions made for that resource are available. The table includes four columns:

      • Submission: shows the version loaded in EcoPortal with the labels next to it. The labels assigned automatically by the portal are parsed (the resource has been parsed), indexed (the resource has been indexed), metrics (the metrics for that resource have been calculated) and annotator (the resource is ready to annotate some text via API or the Annotator tools). EcoPortal indexes the latest submission. The previous submissions will show the "Archived" label, which means that submission will no longer be published;
      • Release date: shows the date (mm/dd/yy) when the new resource was released (manually set by the user);
      • Upload date: shows the date (mm/dd/yy) when the resource was published on EcoPortal for the first time (automatically set by the system);
      • Downloads: permits download of the resource in different formats SKOS, OBO, UMLS, OWL, CSV, RDF/XML, depending on the format of the resource. Furthermore, when more submissions are made for a resource, the system allows an automatic download report (Diff) of the differences between the submitted versions.

    • Views Area

      In this area you can see the views for the selected semantic resource or create a new view. A view provides a manageable portion of a larger semantic resource for localised applications and users. If you are creating a resource as a view it means that:
      • it allows the precise extraction of sub-resources of a larger resource;
      • it allows for localised personalization and use of the larger portion of a resource;
      • it enables the interoperability between large semantic resources and applications. Each displayed view is linked for an easy consultation.

    • Project Area

      In this area you can see the projects using the selected semantic resource or create a new project. Each project displayed is linked for easy consultation.

  • Search

    The Search tool allows you to find a term across semantic resources by entering free text in the “Search…” field and clicking on the “Search” button.
    The system looks for matches in the term name, synonyms, term IDs, and in property values. You can use the advanced search options for including in your search:

    • 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 resource have flagged as being obsolete and which they recommend that people not use. These classes are often left in semantic resources (rather than removing them entirely) so that existing systems that depend on them will continue to function.
    • Semantic Resource Views: search only semantic resource views.

    Moreover, you can narrow your search by selecting “exact matches” and/or “classes with definitions”. Finally, you can type in the "Categories" field to select one or more categories and/or you can also select a set of semantic resources from the "select from list" field. The search will be refined according to only the categories and semantic resources selected.

    Class Search page

    Because of performance concerns, the search returns only the top 100 matches. The search result will display the matched terms and their associated semantic resource. For each search result you can also see (links in green):

    • details: a window with the associated properties of the searched term;
    • visualize: the graph with the nodes of the terms with the path to the root;
    • more from this semantic resource: other terms, present in the semantic resource of the result, are shown.

    To search programmatically see our Search REST API documentation.

  • Annotator

    The Annotator tool allows you to generate annotations by entering or pasting free text in the box and clicking on the “Get Annotations” button. The system matches words in the text to terms in the semantic resources by doing an exact string comparison (a “direct” match) between the text and semantic resource term names, synonyms, and IDs. In addition to the direct matches, the user may expand the set of matches by including matches from mapped terms and from hierarchical expansion. For most semantic resources (OWL and UMLS RRF), the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO semantic resources the hierarchical expansion also includes the part-of relationship. Use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match. To generate annotations programmatically, see the REST API documentation. For more details about the workings of the Annotator, please visit Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14

    Annotator Page

  • Mappings

    The Mappings tool allows you to associate two or more terms in different semantic resources. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. To browse mappings for a semantic resource, select the semantic resource from the drop-down menu. You will then see a table showing all semantic resources for which at least one mapping exists between that semantic resource and the semantic resource you selected. Select a semantic resource from this table to browse the mappings between the two semantic resources. To access mappings programmatically, please see our Mappings REST API documentation.

    Mappings Page

    • Mapping Sources

      Mappings are generated by a LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym. The lexical match involves removing white-spaces and punctuation from labels. Any labels with no more than 3 characters are excluded. These mappings are represented by the mapping relationship "skos:closeMatch". Mapping for terms with the same URI from different semantic resources are represented by the mapping relationship "skos:exactMatch". Mappings between semantic resource terms related by an OBO xref property. are represented by the mapping relationship "skos:relatedMatch". See also OBO mappings.

    • Mapping Relationships

      There are mappings of the following types in EcoPortal:

      • identical, the same:owl:sameAs
        • Definition from OWL): "owl:sameAs" is used to state that two URI references refer to the same individual.
      • related (but not necessarily similar):rdfs:seeAlso
        • Definition (from RDFS): the property "rdfs:seeAlso" specifies a resource that might provide additional information about the subject resource.
      • related match:skos:relatedMatch
        • Definition (from SKOS-REFERENCE): the property "skos:relatedMatch" is used to state an associative mapping link between two concepts; "skos:relatedMatch" is a sub-property of "skos:mappingRelation".
        • Symmetry "skos:relatedMatch" is an instance of "owl:SymmetricProperty"; for bidirectional mappings between <conceptA> and <conceptB> that are "rdf:type skos:Concept":
          • <conceptA> skos:relatedMatch <conceptB>
          • <conceptB> skos:relatedMatch <conceptA>
      • close match:skos:closeMatch
        • Definition (from SKOS-REFERENCE): the property "skos:closeMatch" is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, "skos:closeMatch" is not declared to be a transitive property. The "skos:closeMatch" is a sub-property of "skos:mappingRelation".
        • Symmetry "skos:closeMatch" is an instance of "owl:SymmetricProperty"; for bidirectional mappings between <conceptA> and <conceptB> that are "rdf:type skos:Concept":
          • <conceptA> skos:closeMatch <conceptB>
          • <conceptB> skos:closeMatch <conceptA>
      • exact match: skos:exactMatch
        • Definition (from SKOS-REFERENCE): the property "skos:exactMatch" is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. The "skos:exactMatch" it is a sub-property of skos:closeMatch and, in addition, it is an instance of owl:TransitiveProperty. Also, "skos:exactMatch" is disjoint with each of the properties "skos:relatedMatch", "skos:broadMatch" and "skos:narrowMatch".
        • Symmetry "skos:exactMatch" is an instance of "owl:SymmetricProperty"; for bidirectional mappings between "<conceptA>" and "<conceptB>" that are "rdf:type skos:Concept":
          • <conceptA> skos:exactMatch <conceptB>
          • <conceptB> skos:exactMatch <conceptA>

  • Recommender

    The Recommender tool allows you to get recommendations for the most relevant semantic resources based on an excerpt from a ecological text or a list of keywords The semantic resource ranking algorithm used by the Recommender evaluates the appropriateness of each semantic resource to the input using a combination of four evaluation criteria:

    • Coverage: to what extent does the semantic resource represent the input? The Recommender invokes the Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each semantic resource.
    • Acceptance: how well-known and trusted by the ecological community is the semantic resource? The number of visits to the semantic resource page in EcoPortal and the presence or absence of the semantic resource in UMLS are used to compute an acceptance score for each semantic resource.
    • Detail of knowledge: what is the level of detail provided by the semantic resource for the input data? It is computed using the number of definitions, synonyms and properties of the semantic resource classes that cover the input data.
    • Specialisation: how specialised is the semantic resource to the input data’s domain? This is calculated using the number and type of the annotations done with the semantic resource and the position of each annotated class in the semantic resource hierarchy. The result is normalised by the size of the semantic resource, in order to identify small semantic resources that are specialised to the input data.

    Recommender Page

    For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the semantic resource.
    The default weights used to aggregate the scores can be changed in the advanced options section. Note that besides the output of the semantic resource, which returns a ranked list of semantic resources, the Recommender also has a semantic resource sets output, which allows you to find those semantic resource sets that improve the coverage provided by individual semantic resources. To retrieve semantic resource recommendations programmatically, please see our Semantic Resource Recommender REST API documentation.
    For more details about the workings of the Recomender and to cite it , please visit Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22

  • Vocbench

    The Vocbench tool allows you to manage OWL ontologies, SKOS(/XL) thesauri, Ontolex-lemon lexicons and generic RDF datasets. It is a web-based, multilingual, collaborative development platform, designed to meet the needs of semantic web and linked data environments. VocBench business and data access layers are realized by Semantic Turkey, an open-source platform for Knowledge Acquisition and Management realised by the ART Research Group at the University of Rome Tor Vergata. EcoPortal uses Vocbench as an editor for its resources with a customised version (v.8.0.2-beta.0). The official documentation of VocBench can be consulted at the following link. For a detailed description of the VocBench version for EcoPortal, please refer to the following page.
    Note: At this moment it is not possible to make a single registration on EcoPortal and VocBench. For now, you have to register separately for both services.

    • Login VocBench EcoPortal

      Login VocBench EcoPortal: link

    • Registration VocBench EcoPortal

      Registration VocBench EcoPortal: link

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