Publishing Semantic Resources
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In order to publish a semantic resource on the EcoPortal website, you first need to Create an Account. Once your account is set up, you can Login to start the publishing process.
From the main EcoPortal page, navigate to Tools -> Publish. Alternatively, if you are on the Browsing page (from Tools -> Browse), you may publish your semantic resource by clicking on the "Publish New Semantic Resource" button.
In the resulting form, you will be asked to fill out some metadata about your semantic resource:
- Name: name of the semantic resource
- Acronym: semantic resource acronym
- Administrators: you can select the administrators of the resource. Please note that they must be registered in EcoPortal otherwise they are not shown on the users list. The administrators of the resource can edit the list and make submissions.
- Viewing restriction: you can select whether the resource is to be submitted for public viewing (i.e., all users, even ones not registered on the EcoPortal, may see it on the resources list and may display its contents) or for private viewing only, indicating in the form the accounts that can access it.
- Categories: you can select the categories to which the resource belongs, for example to improve the search tools.
- View: you can check "this semantic resource is a view of" if you want to create a new semantic resource as a view of a selected semantic resource from the dropdown field.
You can also check the "Subscribe to email notifications for new notes" box if you are interested in receiving notifications when users of the EcoPortal community post notes on your published resource.
Once you have filled out the form, click the "Create semantic resource" button in order to create the summary page for your semantic resource. Finally, on the summary page, clicking on the "Add submission” link you can fill in the new submission form where you will be able to specify:
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Format: here you can specify whether you have used the Unified Medical Language System (
UMLS), the Open Biological and Biomedical Ontology (OBO), or the Simple Knowledge Organisation System (SKOS) to create your semantic resource. Alternatively, if you’re uploading anOWLontology, you may choose OWL from the dropdown menu; in this case, and if your annotation properties have meaningful names (e.g.,dc:description), please refrain from changing the specified default properties (Preferred Name Property,Synonym Property,Definition Property, andAuthor Property); map the default properties to your annotation properties only if the latter have coded names (e.g.,BFO_0000179). - Status: submission release status (Alpha, Beta, Production, Retired);
- Release Date: date of issue of the submission;
- Location: you can choose whether to upload only metadata for your resource or metadata, class/concept and properties. For this latter choice, you can upload the resource using the URL or selecting a file on your local file system;
- Home Page: URL of the home page of the resource if it exists;
- Documentation Page: URL of the resource documentation if it exists;
- Publications Page: URL of articles or other products (e.g. book, book chapter, report) in which the semantic resource is referenced (e.g. DOI of a scientific article).
Once you have created the semantic resource submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, please send an email to the support list.
Once the semantic resource has been indexed, you can fill in the submission information by specifying the EcoPortal metadata.
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EcoPortal Metadata Schema are based on the metadata schema provided by BioPortal, and extended with some metadata fields from DataCite Metadata Schema v4.3. In particular, for this latter, we integrated only the metadata needed to obtain the DOI (Digital Object Identifier), which are:
identifier,creator,title,publisher,publication yearandresource type. In the table reported below you can see all the metadata fields used in EcoPortal.Note: The fourth column, Cardinality, indicates cardinality/quantity constraints for the properties as follows:
- 0-∞ = optional and repeatable
- 0-1 = optional, but not repeatable
- 1-∞ = required and repeatable
- 1 = required, but not repeatable
In this metadata form, you can also ask for a DOI for the semantic resource that you are publishing. As you can see in the picture below, there are different options:
- if you do not have the DOI for that semantic resource, you can request it by selecting “None” in the Type field and selecting the checkbox “I want to request a DOI”;
- if you already have the DOI for that semantic resource, select “DOI” in the Type field and enter the DOI in the Identifier field;
- if you have another type of identifier, select “Other” in the Type field and enter the ID in the Identifier field.
If you are logged in as a manager of the semantic resource and you access the summary page in the menu area, the following sections will appear:
- Edit settings
- Add submission
- Edit submission
- This section allows you to change the settings for the semantic resource (e.g., name, administrators, viewing restrictions, categories, etc.). Note that you cannot change the semantic resource acronym, because EcoPortal uses this as a primary key and identifier. If you want to have another acronym, you have to submit a new semantic resource, using the new acronym, and then ask us to delete or deprecate the previous semantic resource.
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This section allows you to update the previously submitted semantic resource with a new version and to update the metadata for the submission. You can update the semantic resource in one of the following two ways:
- if the original submission was set to automatically update from a source URL, EcoPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the semantic resource manager(s) will be notified via email;
- if the original submission was not set to be automatically updated, or if you want to immediately update the semantic resource, you can upload the semantic resource directly by selecting a file from your computer. This will begin the upload process, and schedule the semantic resource to be parsed shortly thereafter. (After successful submission, don't forget to re-enter the URL and settings for the automatic update process, if you want that to be enabled.) Usually, semantic resource parsing is completed quickly, from a few minutes to an hour, except for large semantic resources; semantic resource indexing and automatic mappings occur overnight (Pacific Time).
- This section allows you to update the metadata for the latest submission of your semantic resource, by editing the information on the metadata form. Moreover, you can also replace the URL or the local file if you made a mistake when you have submitted. Once you have edited the form, click on the "Save Submission" button. If you do not change the "Location" settings of the resource, only the changes to the metadata will be saved.
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