Clement Jonquet – clement.jonquet@inrae.fr

Things we are working on

• A consolidated metadata model (still based on MOD, now v2) with value validators, rules between properties, and default/enforced values.

• Multilingual Annotator and Recommender.

• Harmonization of Contacts, Agents, and Users.

• Ability to assign DOI to AgroPortal ontologies.

• Revised notes with GitHub integration and more.

• New social features and notifications.

• Support SKOS collections as primary vocabulary object.

Upcoming releases

• Release 3.6 – Summer 2026 (Refactored notifications & New ontology admin page)

• Release 3.7 – Fall 2026 (New Projects user interfaces and functionalities)

• Release 3.8 – End 2026 (Refactored notes)

• Release 3.9 – End 2026 (OntoPortal federation extension Advanced ontology selector, Federated Annotator and Recommender)

• Release 4.0 – AI enabled services in AgroPortal

Release 3.6 - September 2026

🍂 Autumn Harvest

This release brings agents into search, centralizes the federation of OntoPortal instances, and adds support for two long-awaited features: (i) support of a new ontology formats with the Crop Ontology TDv5 and (ii) support for reified definitions — along with several interface improvements and fixes.

✨ New Features

🔎 👥 Agents are now searchable

AgroPortal describes the people and organizations behind each ontology as agents — creators, contributors, publishers, funders, and so on. Building on the agent-management introduced in v3.2, this release now makes agents directly searchable from the main search box (both on the Homepage and top bar). Typing a person’s or an organization’s name now returns matching agents alongside ontologies, classes/concepts or properties, so you can quickly find an agent and explore the semantic resources they are associated with.

🌐 OntoPortal Alliance/Federation is now centralized by OntoPortal.org

Until now, every OntoPortal instance maintained its own hard-coded list of sibling portals bringing to confusion about which portals were actually active, part of the Federation/Alliance. With v3.6, the list of OntoPortal instances shown on the homepage is loaded from a shared registry centrally maintained by OntoPortal.org. The portals showing up in our user interface therefore stays consistent and up to date across the whole Alliance with no local configuration: newly added portals appear automatically, and retired ones drop off.

Administrators can now also manage federated portals directly from the Site Administration interface. This will make the extension of the Federation way more easy, as portals will not have to change anything to “get federated” with others.

Also added within the Federation: FAIR scores of federated ontologies are fetched and displayed right on the browse page.

🌾 Support for Crop Ontology Trait Dictionaries v5 (TDv5, XLSX)

The plant science community describes traits using Crop Ontology trait dictionaries. Typically those dictionaries (also called Crop Ontologies) were retrieved from https://cropontology.org/ which was acting as the hub for this community. AgroPortal now supports submitting these dictionaries in the latest TDv5 template, directly as XLSX files — no manual conversion needed. The XLSX/TDv5 file is converted to OWL then the normal OWL-API based parsing is triggered.

This makes it far easier for Crop Ontology contributors to publish and keep their trait dictionaries up to date in AgroPortal, using the exact format they already work with and possibly plugging-in their source file directly from GitHub or other external source.

As with any resource, AgroPortal will always allow to download the original source file submitted (here the XLSX/TDv5 file) and the parsing result in RDF/XML syntax, as loaded to the triple store.

🧩 Support for reified definitions within SKOS thesaurus

In some semantic resources (often within SKOS thesaurus) a concept’s definition is more than a plain sentence: it can carry its own metadata — a source, a reference, provenance. When the target of the skos:definiton property is itself an URI, we call this a reified definition…. but unfortunately, even if SKOS specification supports reified Labels (with the SKOS-XL extension) it does not support reified definitions (or any general Notes). Therefore, practices to declare reified definitions varies from in thesaurus/vocabularies, making it super hard for tools like AgroPortal to implement a generic feature, following the standard, as we generally do.

Nevertheless, AgroPortal v3.6 adds support for reified definitions, letting AgroPortal store and display a definition together with this attached metadata (for example, the source it comes from) instead of as a simple text string. The result is a richer, more traceable view of where a term’s meaning originates. When you will see the small icon aside a definition (already used for refified labels), then you can click to get information about the definiton.

As you seen in the AGROVOC example, reified definitions being not typed, we can hardly served them by the API (we retrieve them with a UI trick). But when definitions are typed in the source file by the vocabulary developper as for instance with owl:NamedIndividua, then our API serves them well as we do with any instances. In the following example form INRAETHES, you will then see the types and the {} icon bringing you, as usual, to the corresponding API call.

Attentive readers will have noticed that extracting the actual text of a reified definition requires a heuristic, as no standard defines how to do it. We therefore check rdf:value and a handful of other properties — so make sure your source file uses one of them… or campaign for an extension of SKOS!

🆕 Also new in this release

• Multiple SPARQL endpoints in ontology action icons — quick access to more than

  
  one SPARQL endpoint directly from an ontology’s action icons.

• O’FAIRe URL exposed in /site_config — the O’FAIRe assessment endpoint is now discoverable programmatically.

• Synonyms as compact chips — synonyms are now displayed as compact chips, making them easier to scan on class and Summary pages. See screenshot above.

🐛 Bug fixes

• Available labels are now shown by default instead of identifiers in ontologies with no English labels.

• A new submission can go from a pullLocation to a local file upload or the other way around with no more issue.

• Fixed the ontology page overflowing on small displays.

• Added missing submission breadcrumb translations.

• includedInDataCatalog no longer points to the REST API by default but include the portal URL.

• definitions.ttl is no longer kept after archiving.

• Fixed the “Ontology already exists” error incorrectly linking to BioPortal.

• Fixed a server-side request forgery (SSRF) in the URI resolvability check. With help of our MatPortal collaborators.

Release 3.5 - June 2026

One FAIRness score was good; two are better 🎯

This release of AgroPortal strengthens metadata management, include another alternative tool for FAIRness assessment, and a brand new Statistics page. It also brings several interface improvements and bug fixes.

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New end user features

• 📥 You can now download the metadata of earlier submissions of an ontology, not just the latest one.

• 🔗 A button now gives you direct access to the API call corresponding to the mappings being viewed.

• 👁️ Added an "eye" icon to show or hide your password in forms.

• 📊 Several improvements and new indicators on the portal's statistics page (see below).

New ontology admin features

• 🎯 A new picker lets you select ontology classes directly to fill in the "key classes" (keyClasses) and "example identifier" (exampleIdentifier) fields, instead of typing URIs manually.

• 🏷️ Added dedicated "Subjects" and "Categories" components to the metadata administration page, now clearly distinct from one another.

• 🏛️ The agent creation/editing form now includes search against the ROR registry (Research Organization Registry) to link an organization to its standardized identifier.

• 📅 The "Agent" model now stores and displays its creation date.

✅ Richer FAIRness assessment: now O’FAIRe and FOOPS!

In complement of the O’FAIRe FAIRness assessment methodology (partially) implemented in release v2.2, now AgroPortal also integrates the FOOPS! FAIRness assessment tool developed by UPM as an asynchronous component (non-blocking loading) on the Summary page of an ontology. Whereas O’FAIRe is based on the metadata record of the ontology stored in AgroPortal (i.e., the metadata values seen on the Summary page), FOOPS! is based on the content (data and metadata) of the ontology source file itself.

Both FAIRness assessment scores are integrated in a carousel UI component that allows you to see the to scores computed differently from the two tools. Clicking on the See details button will uniformly shows you the explanation of the assessment as provided by the source tool. For FOOPS!, it is based on the 24 criteria.

Attention: Currently FOOPS! has a default limit to 20mb files, so we have (22/259) ontologies that will fail.

🔧 Improvements & bug fixes

• 📚 Documentation links now point to wiki.agroportal.eu (replacing doc.jonquetlab.lirmm.fr).

• 🔍 The SPARQL endpoint now uses the latest RDF-ready submission.

• 🪵 Improved log configuration and immediate failure (fail fast) when the cache is missing.

• 🇫🇷 The ontology submission form is now fully available in French.

• 👁️ Simplified views display summary — Simplified the display of the ontology views on the Summary page.

• 🗜️ Fixed detection of gzip/zip archives with modern MIME types.

Release 3.4 - March 2026

AgroPortal now runs on INRAE servers!

AgroPortal is an open, community-driven semantic artefact catalogue (we call it also an ontology repository) dedicated to agri-food. Its core mission is to support the management, sharing, and reuse of FAIR ontologies, vocabularies, terminologies, thesauri, etc. to enable semantic interoperability of data and services in these domains. As a key member of the OntoPortal Alliance, AgroPortal contributes to a broader ecosystem of interoperable semantic artefact catalogues built on a shared technology stack. It also plays a central role in the OntoPortal Federation, helping to interconnect multiple domain portals and provide unified access to distributed semantic artefacts, thereby strengthening interoperability across communities. Within the European Open Science Cloud (EOSC) and the Common European Agricultural Data Space (CEADS), AgroPortal serves as a key infrastructure, enabling the discovery, alignment, and reuse of semantic artefacts to support semantic interoperability across data, services, and AI assets.

AgroPortal v3.4 marks an important milestone with the successful migration of the platform to a new domain (agroportal.eu) and its deployment on INRAE infrastructure. INRAE is committed to supporting AgroPortal as a strategic digital common for the institute and, more broadly, for the scientific community, ensuring its long-term sustainability, openness, and role in enabling semantic interoperability across agri-food and other domains.

The 3 main endpoints for AgroPortal are therefore now here:

• User Interface ➡️ https://agroportal.eu

• REST Web service API ➡️ https://data.agroportal.eu

• SPARQL Endpoint ➡️ https://sparql.agroportal.eu

Beyond the infrastructure evolution towards a more robust and maintainable platform, this release include a few interface refinements and enhanced API usability, while addressing several bugs to improve data consistency and system reliability. Key highlights:

• 🌐 Migration to a new domain and hosting infrastructure (INRAE servers)

• 🚀 Improved user experience (UI updates, clearer feature descriptions, better API access workflow)

• 🐛 Bug fixes enhancing data consistency and metadata curation functionalities

• ⚙️ Backend and deployment updates, including configuration changes and additional unit tests for improved reliability

Release 3.3 - December 2025

Happy new year, SPARQL is back!

First, we added a little component on the Homepage for Agents (in place of the Twitter feeds that no one wants to see anymore!). This section now shows a general quick overview of who’s doing what in AgroPortal and calls for discovering more the Agent profiles:

• Total number of agents in AgroPortal (now 1125). Reminder: an agent is either a person or organization related somehow to an ontology. Those are different of the “users” which corresponds to the accounts on the portal. Agents can be browsed here: https://agroportal.lirmm.fr/agents

• The top 5 most active agents. Measured by the number of “usages” i.e., some sort of relation to an ontology as captured by the ontology admins.

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The most important features of this release addresses our SPARQL masters:

• 🎨 Now ontology admins can Edit sample SPARQL queries in the Edit ontology page to specify the queries that will be exemplified –for every users– in the ontology-dedicated SPARQL query editor.

  
  For instances, if interested in AGROVOC, you can see and run 3 queries (inspired from FAO’s) pre-entered as well as running your own : https://agroportal.lirmm.fr/ontologies/AGROVOC?p=sparql

• So if you’re the admin of an ontology in AgroPortal, come over to edit the sample queries.

• 🛠️ In addition of the “ontology-specific” query editors (that are customized to only talk to the corresponding ontology graph in the triple-store), we have integrated a global visual SPARQL Query Editor which helps you compose SPARQL queries for multiple ontologies and also any other objects in AgroPortal (as all the application business objects are stored in the triple-store too). For instances you can query:

  • All the metadata records of ontologies at the same time (e.g., get the publisher of all the ontologies);

  • The whole content of the triple-store (e.g., count the number of sub-classes of BFO_0000003 (“occurent”) across all the ontologies);

  • The graphs of agents, projects or even mappings.

  Similarly than with the dedicated Editors, we have pre-configured a few SPARL queries in the interface that you can easily test to try. You can suggest more. This new page is accessible at: https://agroportal.lirmm.fr/sparql (accessible from the Explore menu).

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📍 For those of you who want to work with AgroPortal’s SPARQL endpoint and not deal with the UI at all, we have (re)made our backend triple-store SPARQL endpoint accessible directly with a read-only Virtuoso interface. This endpoint is accessible at: https://sparql.agroportal.lirmm.fr/ (accessible from the Footer).

These additions make the portal much more friendly for users who want to explore data with SPARQL without switching tools for every ontologies. Plus, the SPARQL endpoint is a nightly-made copy of AgroPortal’s main backend-triple-store (without a few sensitive graphs) so you can play around at no risk ;)

🗂️ This release contains also an important feature related to indexing all AgroPortal semantic artefacts with one “reference vocabulary” itself stored inside the platform. We have enabled a generic selection of a “theme taxonomy” (as DCAT says) in the settings of the portal which allows to select a couple of reference vocabularies hosted locally to index all the semantic artefacts. In AgroPortal we use for the moment AGROVOC for that role. When an ontology developper edit his/her ontology, he/she can now directly pickup controlled terms from AGROVOC in the “Subject” metadata field. This brings more structure to how ontologies are categorized and found in AgroPortal and ultimately we shall also be able to use the semantics of the reference controlled vocabulary for ontology identification. Similar to the Summary page, the three fields Categories, Subjects and Keywords have been regrouped in the “Description” section on the ontology Edition page, and a selector (restricted to AGROVOC) allows to pick-up Subjects from only this vocabulary.

We started to work on a new page called “My ontologies”. Basically this page is a restriction of the Browse page allowing you to see only the ontologies your are an admin off. It includes the same filters so you can quickly find what you’re working on. But it is designed to be faster and more focused on your content. You can access this page either directly at https://agroportal.lirmm.fr/my-ontologies (when logged-in) or via the Personal menu.

Note that this feature does not replace the filtering of ontologies for the whole AgroPortal that a user can customize in his account settings. The “Custom ontology set” will enable you to see and use in AgroPortal only your own custom ontologies of interest, not restricted to the ones you’re and admin off.

Talking about the menus, we have regrouped a set of services and tools of AgroPortal –the top bar was getting to small!– in a new Explore menu that gathers several pages:

• Agents

• Landscape (still not yet refreshed to the new UI framework)

• Groups & Categories

• SPARQL Editor

• AgroPortal Statistics

⚙️ In the back and and admin side, for OntoPortal administrators, we have integrated a component called Flipper which lets us toggle features on/off dynamically. These flags are admin-only and persist immediately in the UI, making testing and rollouts smoother. For example, if another OntoPortal instance does not want to showcase the Agent profiles, this can now be deactivated at the click-of-the mouse with Flipper. In collaboration with OntoPortal, we are going to use Flipper to enable a quick and easy customization of a new OntoPortal instance.

In this release, we also squashed a bunch of bugs and improved the overall feel of the portal:

• 🐛 500 errors fixed — various backend errors related to licenses, filters & federation workflows are now resolved.

• 📜 Better license handling — if something goes wrong with licenses, you’ll now see friendly error messages instead of generic failures.

• 🌍 Language flags display correctly — e.g., multilingual support like AGROVOC language tags now show as expected.

• 📊 Correct metrics for large ontologies— metrics calculations and display are fixed and reliable.

• 🧭 Admin tabs reorganized — the layout in the administrative interface is tidier and easier to navigate.

Release 3.2.1 - September 2025

This release contains mostly bug fixes and performance optimizations… but a couple of changes that would interest those closely monitoring the metadata records of their semantic ressources in AgroPortal:

• In the Browse page, by clicking “Show my ontologies only”, logged-in users can now filter out the list of ontologies to see only the ontologies they are admin for (#1158). The right combination of the “private only” and “my ontologies” filters allow to quickly get the list of ontologies a user is involved in.. either as an admin, or as a user with granted access to private ontologies.

• This feature complement and does not conflict with the “Custom ontology set” historical feature that, as a reminder, allows to get all the user interfaces and services in AgroPortal for only a subset of selected ontologies (see “Account settings”).

• AgroPortal homepage will now load faster as the metrics are lazy-loaded and a few other optimization have been done.

  
  

With this release, we changed the metadata extraction from the source file to avoid extracting again and again (version after version) metadata values that would pollute the metadata values already curated. We introduced a mechanism to declare which properties will be extracted only once, during the parsing of the first submission of the ontology. In other words, if a source file contains dc:creator property to declare the creators of an ontology then the values will be extracted the first time AgroPortal see the ontology, and new agents will be created (with whatever information AgroPortal founds in the source file). Later, the ontology admin or the curation team will consolidate the agents in well formed structured agents in our database or merge them with already existing agents. Once this is done, to avoid re-creating agents that would need curation again, the property dc:creator would be ignored from subsequent parsing. We apply now this behaviour to multiple metadata properties when a curation is done e.g., License, Publisher, Keywords, Subjects, etc. Check out the back end call describing AgroPortal submission metadata: https://data.stageportal.lirmm.fr/submission_metadata and search for “extracted: once” to see the complete list of properties.

Release 3.2 - June 2025

Agents are everywhere except in the new MOD-API!

This release marks the introduction, in the front-end, of a brand new set of user interfaces with new agent profile pages and in the backend, the first implementation of a MOD-API. It also comes with important updates on the backend, improvements in security, bug fixes, and performance optimizations.

• We developed multiple user interfaces to search and browse agents (Persons & Organizations) in the AgroPortal database (#963). Agents were introduced in the backend & API with release v2.7 (https://data.agroportal.lirmm.fr/agents), but there was no corresponding user interfaces. Now when browsing an ontology, one will be able to click on the agent badge and move to the corresponding agent profile page. The agent profile shows the agent information as well as role in ontologies and collaborators (i.e., agents with the same affiliation) if on a Person page or affiliated agents if on a Organization page. A “Related themes” section shows an aggregation of the Categories, Subjects and Keywords of the ontologies related to the agent.

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  The list of all agents in AgroPortal can be accessed by the “Support” menu in the top right corner.

  
  

  
  
  

  This page allows to search and filter agents in a table to lookup the Person or Organization of interest.

  
  When logged in, this page allows to create new agents and associate them to ontologies, or to edit/delete agents previously created by a user.

  
  Number of '“Usages” (i.e., role in ontologies) is informed by a specific column. When an agent is “Not used”, it means it is not directly associated to an ontology, but it could be associated to an Organization or another object in the repository.

• We have curated the whole agent database consolidating agents (with ORCIDs / RORs and affiliations when possible) and removing the duplicates. AgroPortal counts more than 1100 agents today. You may still see duplicates or uncurated entries because agents are still automatically extracted from source files which constantly re-create already curated agents if a new submission is uploaded or pulled. We are working on this.

  
  

• At the metadata level, we have harmonized and consolidated: Categories, Subjects and Keywords. Now each ontology metadata is structured around three complementary descriptors:

  • Categories: broad domains selected mainly from the UNESCO Thesaurus (see release v. 2.10) and restricted by AgroPortal, ensuring a harmonized top-level classification.

  • Subjects: finer-grained, controlled descriptors expressed as URIs from one or more selected vocabularies hosted in the portal (in our case AGROVOC only for now), used for precise indexing and retrieval.

  • Keywords: free-text terms (one per value, not lists), eventually drawn from a local folksonomy, that enrich discovery but must not duplicate existing Categories or Subjects.

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• We have completed the the first implementation of a MOD-API (v. 1.0) –a DCAT2-based shared specification of a web service API for semantic artefact catalogues– based on Metadata for Ontology Description and Publication Ontology (MOD) developed within the FAIR-IMPACT project. MOD-API implementation supports all the calls in the specification allowing to list artefacts, distributions, records, content of artefacts (classes, concepts, properties, etc.) as well as search data and metadata. The MOD-API is described with Swagger: https://data.agroportal.lirmm.fr/mod-api/doc/api

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  MOD-API does not replace the historical API which is still here and drive the whole platform user interface, but MOD-API offers a new endpoint compliant with an independent specification which can be implemented by multiple ontology repositories or Semantic Artefact Catalogues and enable their interoperability.

  
  

• We have implemented a new admin page for “Site description” (#929) to edit graphically the values returned by the new MOD-API call describing the catalogue (mod:SemanticArtefactCatalog) at the root endpoint (https://data.agroportal.lirmm.fr/). This page allows to describe AgroPortal itself (e.g., description, title, contributors, funding, etc.) and also specifies some parameters to support the OntoPortal federation (e.g., logo, colors, federated portals, etc.).

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  Eventually, this “Site description” page will allow any new OntoPortal deployer to describe and parametrize its own ontology repository only manipulating the user interface (and no more configuration files).

• With this release, we have also moved the software to Ruby 3.2, added Sentry to monitor the platform and finished the support of the French localization.

On the publication/communication track, we have published a short article, In French, at the IN-OVIVE 2025 workshop about the use fo AgroPortal at INRAE (https://hal.science/hal-05077024) showing the integration of AgroPortal (or the partner project EarthPortal) in 5 information systems.

Release 3.1 - March 2025

Bye bye 4store, AgroPortal is now running on Virtuoso

🔧 This release marks a significant evolution of the AgroPortal platform, both in terms of its architecture and technical foundations, that improve maintainability, performance, and flexibility of the platform.

• The platform is now triple store agnostic. While it previously relied specifically on a particular backend (i.e., 4Store), the architecture has been generalized to support various RDF triple stores. This work –started by our partner at Stanford with BioPortal backend change to AllegroGraph (end of 2024)– was continued and generalized by the AgroPortal/BiodivPortal team for an agnostic integration of alternative or multiple RDF backends. OntoPortal can now run on either 4Store, AllegroGraph, Virtuoso or GraphDB. AgroPortal now runs on Virtuoso since February 2025.

• We have upgraded the entire codebase to Ruby 3. This ensures compatibility with modern libraries, better performance, and improved security. We have completed our user interface test library, including for the federation features.

• All internal and external dependencies have been reviewed and upgraded to their latest stable versions. This has significantly reduced technical debt and modernized the stack. We have also cleaned updated our lookbook (#920) to ease the reuse of graphical components when building/extending the UI.

  
  

With the backend changed, we are still working on making AgroPortal’s SPARQL endpoint accessible again at: https://sparql.agroportal.lirmm.fr.

This version includes also the first steps toward supporting the MOD-API –a shared specification of a RESTful web service API for semantic artefact catalogues– based on Metadata for Ontology Description and Publication Ontology (MOD). More information will come with AgroPortal 3.2.

This release also includes small features, technical improvements and fixes such as:

• The ability to display private ontologies on the user Account and Browse page (#902)

• We have created a graph endpoint service (https://data.agroportal.lirmm.fr/admin/graphs) to list, create and delete our graphs, for better management and maintenance or our backend data.

• We have added a SPARQL query logging system to monitor the activities on the SPARQL endpoint.

• We have cleaned many zombie mapping graphs and implemented solution to prevent their creation.

Release 3.0 - November/December 2024

OntoPortal Federation joint release

This major release brings the federation feature to OntoPortal, enabling users to browse ontologies and search for classes and concepts across multiple federated portals. This is a joint release with EcoPortal, EarthPortal and BiodivPortal i.e., each portal is now connected to each other and displays some content from the others.

Technically speaking, this federation is done “at the user interface level” as the backends and APIs of each portal are already the same. The federation architecture is rather simple, based on the project Ontology API Ruby Client which has been changed to query and aggregate the results from multiple backends (as illustrated). The user interfaces have been significantly changed to handle the results coming from different portals while helping users to understand what is going on and addressing performance issues.

The federation of AgroPortal with other OntoPortal-based ontology repositories has multiple technical and collaborative dimensions summarized hereafter:

Federated Browse page

The introduction of federated browsing in AgroPortal 3.0 marks a significant enhancement in the way users explore ontologies (see #621). This feature allows users to seamlessly discover ontologies not only from AgroPortal but also from other federated portals, today: EcoPortal, EarthPortal and BiodivPortal. The total number of ontologies gathered by all the 4-federated OntoPortal is currently 376! Federated results are integrated alongside local ontologies, preserving the familiar interface while expanding the scope of discovery. All filters remain functional within the constraints of the metadata available from each portal, ensuring relevance and usability. Thanks to the federation of the Categories (see below), numbers can be calculated with unified categories coming from each federated portals (only parent categories).

Portal-specific parameters, like Groups or Private settings, are excluded to maintain consistency across federated results.

Users can activate federation through a straightforward selector, and the visual design incorporates the portal's color code and small logos to clearly distinguish federated ontologies. The number of ontologies retrieved from each portal are automatically updated with filters or parameters selected.

When clicking on a ontology result, the user will either stay on AgroPortal if the ontology found is hosted locally or move to another portal in the federation if not. Duplicates are identified by matching acronyms and URIs, and only one unified ontology card is displayed, aggregating analytics like notes and projects and listing logos for the set of portals where the ontology can be found.

• If the duplicate ontology is found locally, the card will always feature AgroPortal information and allow users to continue locally to explore the ontology.

• If the duplicate ontology is not in AgroPortal, the card will reflects the primary portal's color. The primary (or canonical) portal for an ontology is found to be the one with the highest number of pull location references from other portals in the federation (#770).

For performance scalability, the Browse page incrementally loads results from federated APIs; only local ontologies load by default followed by federated results if selected providing a seamless user experience while making aware to the users that additional content is being loaded.

Federated Search

The federated search feature in AgroPortal 3.0 (see #739) introduces a new dimension to ontology exploration by enabling users to search concepts and classes not only within the local portal but also across other federated OntoPortal instances. This functionality allows users to discover semantic resources hosted on remote portals while maintaining a consistent user experience. Search results from federated portals are visually distinguished using their respective color codes, and clicking on these results redirects users to the source portal for more detailed exploration. The search remains local by default, with federation being an optional feature activated through a simple selector in the Search options.

The number of results by portal is displayed and managing duplicates is done in a similar approach than on the Browse page. Considering search results scores are not normalized between portals, to rank and mix results effectively, a cosine similarity is employed between the search query and the retrieved classes/concepts labels to balance relevance across portals.

Federated User Interfaces and Portal description

With this joint release, the federated portals have adopted similar user interfaces and look and feel with a specific color theme so that users going from one ontology repository to the other are not lost and found similar interfaces and functionalities. EcoPortal, EarthPortal and BiodivPortal have then embraced the changes done in AgroPortal releases 2.7 series related to new UI/UX.

Since release v2.7.4, AgroPortal’s homepage includes a component to link to other public portals in the OntoPortal Alliance. Now, when mousing over the logos, the portal with which AgroPortal is federated will display some information about them such as a description and the number of ontologies available (see #744).

This functionality is implemented by means of a new web service endpoint implemented by each federated portal to describe itself. Going now to https://data.agroportal.lirmm.fr/ will return a JSON-LD description of AgroPortal that other portals can consume.

Eventually, the description of AgroPortal (and any OntoPortal) will be based on the mod:SemanticArtefactCatalogue object specified by the MOD v3.2 metadata vocabulary.

Federated Categories

All the portals in the federation now use a unified general disciplines vocabulary –the UNESCO Thesaurus– to describe each portal categories. This allows for an easier comparison of the disciplines covered by each portal and enable to federate the filtering of ontologies by categories in multiple AgroPortal views.

Consequently, AgroPortal has now changed all its categories to follow this shared approach. We have picked up 41 categories (organized as top categories and sub categories) from the UNESCO Thesaurus and 1 from AGROVOC. These categories are shown in multiple views in AgroPortal with “shortnames” and are mostly used to: (i) assign categories when editing on ontology; (ii) select ontologies in Browse page or Advanced ontology selector.

We have re-assigned every ontologies or vocabularies in AgroPortal to those categories / disciplines. This work has been done mostly manually and is currently being curated, but we suggest ontology developers to double check if the new categories assigned to their resource are appropriate and/or if any other ones are missing. We welcome feedback on this new organization of AgroPortal’s categories and are expecting some adjustments in the months to come.

Federated Documentation

We now provide a user guide (https://ontoportal.github.io/documentation/) organized in a way that federates the content from each portal documentation. In other words, if one portal has documented something that is generic to any OntoPortal-based ontology repository, a specific portal documentation can import this content, without re-writing it, in its own custom portal user guide. Documentation is available for the moment for EcoPortal and EarthPortal and the default OntoPortal software. When browsing the documentation, one will always stay “within the specific documentation of one portal” unless clicking at the bottom of any page to switch from one documentation to the other.

AgroPortal documentation will soon be moved to the Federated Documentation but users can already benefit from generic documentation pages written by other OntoPortal partners.

The OntoPortal federation is built in a way that is totally configurable, each portal can select the desired other OntoPortal-based instances to federated with (and it does not have to be symmetric) and the user interfaces are not changed if federation is not used. By doing so, OntoPortal master code user interfaces can now evolve with/without federation. To address downtimes, we have implemented a status check which disables the selection of a federated portal if it is not reachable. Ultimately, a time out will avoid AgroPortal to wait for ever results from a federated portal.

Eventually, in subsequent releases, OntoPortal federation will be completed with additional federated features such as: metadata synchronisation (for duplicate ontologies), federation of users, agents, mappings as well as key services such as the Annotator and Recommender.

In addition, AgroPortal 3.0 includes significant feature enhancements, bug fixes, and user experience improvements some detailed below:

• Allow multiple parent Categories (#772). Soon, we will use parent Categories to ease the description/selection of ontologies.

• Add Details sub-tab and API contextual button in Properties, Instances, Schemes, and Collections (#754).

• Update concept mappings table UI (#798).

• Reorganized the Homepage and Summary page by moving the metrics section to a more prominent position (#747)

• Enable and disable Twitter section on the Homepage.

• Migrated Label Ajax, Stimulus, and jQuery code to Turbo (#821).

• Improved Agent search functionality (#837).

• Fix zombie mappings counts (#167).

• Add unmapped, range and domain attributes for properties endpoints (#89).

• Parse xml diff files into a model (#161) and add submission diff endpoint (#95). More features related to diffs coming in next releases.

• Add mappings to Ontologies contextual API links (#158).

• Add Brazilian to the enforced values of submission language attribute (#157).

This release goes along a huge parallel work of re-alignement of ontoportal-lirmm branches (used for AgroPortal and now all the portals in the current federation) with the upstream ontoportal code so that anyone will benefit from the new functionalities originally developed for AgroPortal and/or for the OntoPortal federation.

Release 2.10 – September 2024

Properties have now properties

This release introduces two new important features.

• For a long time our users where wondering why Properties in AgroPortal would not be displayed/manipulated as Classes/Concepts, especially why properties describing the properties were not available especially domain (rdfs:domain) and range (rdfs:range). This is now done. We have now modified the “Property” object in our backend model that have properties. A “Raw data” panel will display all these properties in the user interface. In the bellow example, the property “Assay measures characteristics” from RO is described: https://agroportal.lirmm.fr/ontologies/RO?p=properties&propertyid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0009006

  
  
  

Our model for properties maps Preferred name, Definitions, Parent property, Domain and Range. Which means that for every ontologies in AgroPortal, users can uniformly access and query these 4 informations,

independently of the way they were defined in the original source file.

The URL in the browser will directly bring you to the property and we will have soon a small ({}) button that will bring you to the corresponding API Web service call. In the previous example, the API call is: https://data.agroportal.lirmm.fr/ontologies/RO/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0009006?display=all

• The second feature of this release is a new web page to describe Groups and Categories: https://agroportal.lirmm.fr/groups and https://agroportal.lirmm.fr/categories. Groups and Categories are used to classify ontologies and filter them out in the Browse page. Groups are also synchronized with Slices (see release v2.8.1). We previously had an API web service call to read/write groups and categories, but no corresponding page in the user interface.

The page shows the description of groups/categories and provide links to the subset of ontologies within a group/categories in the Browse page.

This page goes along with a corresponding administration page (see release v2.7) that can be used by administrators to edit and create Groups/Categories. This feature will be quickly shared with other OntoPortal instances, and in release v3.0 we will have brand new Categories based on the UNESCO nomenclature for fields of science and technology as will EarthPortal, EcoPortal and BiodivPortal. The Groups and Categories web page can be open from the top right “Support” menu.

Release 2.9.1 – August 2024

This release focuses primarily on bug fixes and enhancements to existing features. Our main priority has been addressing issues related to the agents, ensuring a smoother and more reliable experience. We also fix an issue with Search service introduced when we implement multilingual support (now, if not using languages, the search service is backward compatible).

With this release, our users will also notice the arrival of a new Cookie banner. The banner needs to be accepted once to disappear. It acknowledges user acceptance of our functional cookies described in the Terms & Conditions.

Release 2.9.0 – July 2024

Cool URIs for the Semantic Web AgroPortal resources 🔗

The main focus of this release is a new AgroPortal service for URI management: we introduce an internal system for resolving and dereferencing URIs for each RDF resources within an ontology (ontologies, classes, concepts, properties, individuals, etc.).

• For each URIs visible in the user interface, AgroPortal tells if this URI is resolvable (i.e., will actually resolve to a Web ressource if requested via HTTP) and negotiable (i.e., support HTTP content negotiation and return alternative formats). One may “click to see details” and be moved to AgroPortal new Check Resolvability small application described after.

• For each URIs (ontology or resource within the ontology), AgroPortal now generates automatically an analog ‘AgroPortal URI’ that does support HTTP content resolution and negotiation in 4 formats (JSON, XML, Turtle, Ntriples) and of course HTML, bringing then the user directly to the corresponding Web page in AgroPortal (#547, #568). This “fake” URI does not replace the original URI, and is not made to to be used externally except to redirect the original URIs (when they are not resolvable and/or negotiable).

  • When called on a resource within an ontology, this fake URI will return only the triples related to the queried ressource i.e., triples following the patterns < resource P O> and <S P resource> based on what we have in AgroPortal’s triple store. This behavior does not work for URIs using a # to identify the code of the resource; in this case we return the full set of triples within the ontology.

  • When called on an ontology, this fake URI, if negotiated, will return:

    • the Summary page (if HTML requested);

    • the metadata record (if JSON requested);

    • the RDF/XML file produced systematically by AgroPortal from the original source file (if XML requested);

    • an automatically generated tabular format (if CSV requested);

    • the original source file in Turtle or Ntriples (if one of this format is expliclity requested and the source file was available in this format).

    • If no format is requested, it’s always the original source file (whatever format) that will be returned.

• On the ontology Summary page, on the AgroPortal URI the symbol (chain) –when clicked– will display the instructions (for Apache and Nginx Web servers) to communicate to the person in charge of the domain name redirections so it’s easy for ontology developers to ask for a simple redirection and trust AgroPortal to manage the resolution and negotiation of all URIs.

• Now that we can return extract of RDF in multiples formats, when browsing a resource, we added buttons in the “Raw data” section to see/download what will be negotiated.

  
  
  

With this release come a new "tool box” of small app/services we have implemented to support the previously described functionalities. Clicking on Products>Tools in the footer, users will get access to:

• Search content: In the future, this will allow to search with an URI or label across all of the indexes behind AgroPortal (cf. release 2.8.0);

• Content converter: allows to search and retrieve the content (triples) related to any URI in AgroPortal assuming we known in which ontology (graph) search (#511). Indeed, all the URI management features are “ontology" specific” which means that even if an URI is re-used in multiple ontologies in AgroPortal, the URI is always considered specific to an ontology and the content may be different.

• URI resolvability checker: for a given Semantic Web URI (whatever its in AgroPortal or not), this service checks if the URI is resolvable and support content negotiation.

Release 2.8.1 – July 2024

This release is mostly for bug fixes 🔨 and small enhancements. However, two important things are to note for this release:

• We have put back the Slices links on the Home page (#598) ⚡️. As a reminder, slices allow users to interact (both via API or UI) only with a subset of ontologies in AgroPortal. If browsing the slice, all the portal features will be restricted to the chosen subset, enabling users to focus on their specific use cases.

  • The links show you the name of the Slice and the number of ontologies or semantic resources in the Slice. To browse a restricted AgroPortal to the Crop slice, click here: https://crop.agroportal.lirmm.fr/

  • 
    
    

    On AgroPortal, slices and groups are synchronized, so every group has a corresponding slice displaying only the ontologies from that group. In a near future, we will have a page to visualize the groups and categories within AgroPortal.

  • A yellow banner clearly shows the users if they are browsing a slice in AgroPortal. In such a case, the features of the repository (ontology listing, selection, annotation, search, etc.) are all filtered out to the subset of ontologies within this Slice/Group.

    
    
    

    
    

  
  

• 
  We have implemented a mechanism allowing to distinguish the objects reused from other ontologies in the left panel (tree view, list and date view) for whatever objects (classes, concepts, properties, instances, schemes and collections)(#650).

• 
  

Where Protégé historically does this with bold, we used a small recycling icon on the right hand side of the resource. For instance when browsing the hierarchy of an ontology (here AGRO on the right), a small recycling icon indicates classes reused from another ontology.

To implement that distinction, we implemented a few heuristics to be able to distinguish between URIs defined in the main namespace of the ontology from the ones defined in another name space. We rely on two metadata properties:

• First, the Preferred namespace URI (vann:preferredNamespaceUri) which gives us the name space URI used for the objects defined within the ontology. In the case of AGRO it is “http://purl.obolibrary.org/obo/AGRO_”.

• And as an alternative, Identifier pattern (void:uriRegexPattern) which tells AgroPortal the regular expression used to structure the URIs within an ontology. In the case of AGRO it is http://purl.obolibrary.org/obo/AGRO_[0-9]{8}

• Complete list of bug fixes and small enhancements can be seen on the technical release notes on GitHub, mostly:

  • We remove the constraint of having an owl:Ontology object within a SKOS source file to distinguish the main scheme.

  • Fix the URL error in the new Note email notification. Soon these notification will bring ou back directly to the note within the ontology and not out of all context as now.

Release 2.8.0 – June 2024

Index them all and search anything anywhere 🔬

• Enhanced search features: We now index much more things into our Solr index (atop the triple-store): not only classes/concepts but now also properties, individuals, collections, and schemes. At the admin level, we made all the indexes parametrizable (#567) and we made the Homepage and top bar search boxes search everything indexed (#505) with a nice and easy auto-completed search tool that allows either to reach out directly to an identified object (first options proposed) or either move to the Search page or Browse page.

We are expecting this new feature to significantly change the way users interact with AgroPortal since this is not necessary anymore to go thru the Browse or Search page before digging into the content of an ontology. Plus, this also searches individuals (aka. instances) which was a desired functionality expected since a long time.

• We have also added specific small search boxes on each pages showing an ontology or semantic resource content: in addition of classes/concepts, we have now a “Jump to” box for the tabs Properties, Instances and Schemes/Collections when relevant (#550). Following the user interface evolution done in releases 2.7.x, we have also rebranded the user interfaces of these tabs (#581, #596).

With these changes related to search and indexing, we have now also created indexes for agents (introduced in v2.7.0) and metadata so we are thinking about new features based on these indexes to come later.

This release also includes some backend changes: (i) updated SPARQL client component (#1); (ii) continued to prepare the multi-backend support (#58, #135, #73, #22); (iii) enhanced SOLR integration (#58, #135, #73) and more. We also did a major performance improvement for the Browse page with a better caching of the results, giving a response time on average of 0,7s (#575, #572) as well as numerous bug fixes.

Release 2.7.6 – June 2024

Mappings as bubbles! ✨

This release is to announce that we are mostly finished with the user interfaces re-modeling —which was the focus of the 2.7.x releases— with a new user experience enabled by AgroPortal’s new Mappings page, adding a better visualization of the mappings in form of cloud of bubbles (#538, #569, #574) in addition of the Table view.

In the previous example, each bubble is an ontology where the size represents the overall number of mappings in AgroPortal’s mapping repository. By clicking on “SO” one can see the other ontologies mapped to SO with the gradient of green. And finally, see the mappings by clicking on another bubble. Notes that the two visualizations (Bubbles view and Table view) stays in sync, so one can go from one to the other without loosing the context.

This release also goes with other UI related work:

• the Admin page uses now use vertical tabs (#566);

• our UI tests continues to be completed, now with Recommender (#599).

Release 2.7.5 – May 2024

This release is to announce you that we have now Terms and Conditions available on AgroPortal footer.

Direct link is : 🗽Terms & Conditions

From now on, any account created on AgroPortal will have to accept these terms and conditions.

IMPORTANT: If you already have an count on AgroPortal (which is the case of most of the persons on agroportal-users@lirmm.fr list) the Terms and Conditions will be considered accepted unless you request the deletion of your account to agroportal-support@lirmm.fr.

Any feedback about Terms and Conditions is of course welcome. We will certainly update the T&C (this version is from March 2024) in the future and announce it on the agroportal-users@lirmm.fr list.

Release 2.7.4 – April 2024

This release includes several new features described hereafter:

• This sub release of v2.7 continues the implementation of new user interfaces with a new design of the Annotator and multiple small pages/views here an there.

• We have implemented what we call in the OntoPortal Alliance, the very first step of the federation of our portals (coming with v3.0): we now list and link on AgroPortal homepage all the other current public and open repositories built with the technology maintained by the Alliance.

  
  
  

• We developed an advanced ontology selection component that enables, each time ontologies need to be picked-up, to easily select multiples ontologies filtering them with metadata properties (groups, categories, keyword, natural languages, etc.)

  
  
  

• Don’t learn our API calls, just follow the API call buttons: we added a bit everywhere within the user interface a little contextual button that brings you to the API call corresponding to the page or content you’re currently see.

  
  
  

This release also include multiple technical improvements and fixes: https://github.com/ontoportal-lirmm/bioportal_web_ui/releases/tag/v.2.7.3

Release 2.7.3 – Feb. 2024

This release includes several new features described hereafter:

• We continue the implementation of new user interfaces with a new design of the Search, Recommender and multiple admin pages.

  
  
  

Note that searches are now captured within the URL so anyone can copy/paste a search call and reproduce it easily: https://agroportal.lirmm.fr/search?q=leaf+area+index&lang=all&ontologies_list[]=PO&ontologies_list[]=TO&ontologies_list[]=TOP&ontologies_list[]=CO_321&require_exact_match=true

• We know URIs are important and have started developing new services for a better support of URIs and content negotiation for our users. However, we are not responsible of the URIs used by developers to identify their ontologies and ontology content. We have now a URI resolvability checker that will for every URI displayed in AgroPortal let the user knows if that URI is resolvable and support content negotiation. A button aside the URI also helps to quiclky copy/paste the URI to use it outside of AgroPortal.

  
  This service is available “on it own” for anyone to test any URI belonging or not to a resource in AgroPortal: https://agroportal.lirmm.fr/check_resolvability

• From the “Export all metadata” link on an ontology Summary page, one can now export metadata to multiple formats: CSV, XML, JSON, N3. We will soon refactor this mechanism to support multiple export profile: MOD, DC/DCAT, Schema.org, DataCite, FAIRsFAIR, etc.

• We have added a SPARQL query user interface dedicated to every specific ontologies. This new feature uses Yasgui to enable anyone to fire a SPARQL query automatically restricted to graph of the corresponding ontology in our triple-store. Yasgui really eases the writing of queries by auto-completing namespaces.

  
  
  

This feature will soon be enriched with prepared query examples that will facilitate the discovery and learning of SPARQL to non expert users. We will eventually have a SPARL query interface for the complete AgroPortal backend knowledge graph enabling to query cross ontologies and possibly using the mappings between the ontologies.

• We have now a new Web page showing AgroPortal metrics and statistics: https://agroportal.lirmm.fr/statistics

  It shows the evolution of the number of ontologies, users, projects and visits since the first release of AgroPortal in June 2015!

• We are improving the representation of agents (ontology creators, contributors, publishers, etc.) in our backend. We encourage the use of PIDs from ORCID and ROR.

  
  

• New admin features for analytics and monitoring. For AgroPortal administrators, we have created a new Web page to facilitate usage analysis. This page shows us multiple indicators such as the total number of ontologies (including with errors), the number of users and visits of the current month. It also helps us monitor the most accessed pages.

  
  
  

When integrated in the main OntoPortal codebase, we believe this page will help multiple groups administrating an OntoPortal installation to follow what’s going on on their platform.

This release also include multiple technical improvements and fixes, see more details here: https://github.com/ontoportal-lirmm/bioportal_web_ui/releases/tag/v.2.7.3

Release 2.7.0 – Dec. 2023

A fresh look at the now multilingual AgroPortal ✨

This release includes 3 major functionalities (hence supersedes v2.5, v.2.6), on which the AgroPortal team has been working on in 2023.

1- Multilingual content support and internationalized user interfaces. AgroPortal user interfaces and corresponding APIs can now serve multilingual content if correctly defined in the ontology source file; users can decide to display one specific language or show the values in all languages.

• Multilingual or language-specific search. We now index labels in all languages (including multiple preferred labels) and enable search either per language or overall.

• Internationalization of the user interfaces (independently of the content of the ontology). We have done French (in progress) and setup the code to use “locale” files to enable future language.

  
  

  
  2- Brand new users interfaces. We have refreshed and modernized the most important user interfaces in AgroPortal. We are still working on migrating all our views. Sometimes, we have revisited the user experience, but the design has mostly remained similar.

• We have simplified the ontology submission process by grouping everything into a unique workflow.

• We have completely remodeled the Summary page enabling our users to visualize key information right away while still providing ways to know in-depth information about a resource. Our challenge was to effectively present over 100 metadata properties! Here is an example with the ANAETHES.

  
  
  

• Similarly, for the metadata edition page, we adopted a new tab-based approach and allowed editing of both ”ontology” and “submission” properties at the same time.

  
  
  

• In addition to the redesign, we have adopted new technological approaches and conventions and built the UI around a “design system” that could be customized by different portals using the underlying OntoPortal technology. For example, the Browse page has been revamped. All operations are now handled server-side to enhance performance, achieved through result pagination. This gives us now URL matching the filters activated by users enabling them to easily share the filtered list as links e.g., https://agroportal.lirmm.fr/ontologies/?search=plant&hasFormalityLevel=Thesaurus&show_retired=true&format=OWL,

  
  3- A better support of person and organization metadata values. We introduced “Agents” as a new object in our backend models –which can either be instantiated as a person or an organization following the FOAF specification– that we use to store the values of 7 metadata properties (creators, contributors, publishers, sponsors, etc.).

Agents (distinguished from Contacts and Users) are the same over all ontologies and are selected by auto-completion.

In addition, we have a new API endpoint to serve agents: https://data.stageportal.lirmm.fr/agents.

We also have a new administration feature for agents enabling an admin user to manage and curate persons and organizations globally.

In the future, this new entity will allow us to rethink notifications, implement new social aspects for AgroPortal, and support new queries e.g., Get me all the ontologies where Clement is “involved” as a person? Get me all the ontologies created by persons working at INRAE.

Other new features in this release include:

• New metadata administration tool allowing editing metadata properties in bulk (for multiple ontologies or submissions at the same time).

• New administration features for groups and categories enable a new OntoPortal admin to quickly setup its portal.

• Multiple Single Sign On options including login with GitHub, Google or ORCID credentials, or a configurable Keycloak protocol.

• Refactor error notifications.

This release also includes technical improvements and bug fixes such as:

• Add Docker images of the AgroPortal/OntoPortal stack, published Docker hub, and GitHub packages.

• Multiple monitoring tools (Newrelic, StatusCake, BugSnag) and compliance with Google Analytics 4.

• Multiple code evolution: using Hotwire, decreasing the use of JQuery and Javascript, removing Angular leftovers, etc.

• Implemented tests for the UI code.

• Multiple measured time optimizations (and more to come!) e.g., Summary page, submission edition, Landscape.

This release introduces a technology switch responsible for rendering our content, resulting in a reduction of 70k lines of UI code, mostly by migrating some old JS code to either a new native JS code or converting it to server-side rendering using Ruby on Rails combined with Hotwire, harmonizing and modernizing our code base. Though this set of code refactoring may not be immediately visible and operates more behind the scenes, it allows us to envision future features and developments that were hardly imaginable before.

The full list of changes (front-end and backend) is available on the corresponding tag GitHub page. We are currently working with the OntoPortal Alliance to merge back our features in the main OntoPortal code.

Release 2.4 – Dec. 2022

A state-of-the-art tool to browse and visualize SKOS resources

This release is mostly focused on a set of new state-of-the-art features for supporting SKOS resources in AgroPortal. For semantic resources in the SKOS format, we have completed the AgroPortal model to include all the objects in the SKOS specification such as Scheme, Collections, and SKOS-XL Labels. We have created new user interfaces to visualize these objects in AgroPortal and re-invented how to browse concepts. All together, these features make AgroPortal a fully SKOS compliant platform which is certainly one of the most advanced SKOS browsing portal. In summary, users can now:

• Visualize the list of Schemes defined in a SKOS resource. AgroPortal will also distinguish one main scheme from the others. We recommend developers to use the SKOS resource main URI to identify the “main” skos:ConceptScheme and also to type it with owl:Ontology to allows us to distinguish it from the other schemes.

• Visualize the lists of Collections defined in a SKOS resource and count the numbers of concept members. For instance, collections defined in BIODIVTHES:

  
  
  

  
  

• Visualize concepts with 3 different approaches:

  • Hierarchical, by selecting the scheme(s) to browse. The hierarchy tree will always refresh to display only the selected scheme(s) and selected collection members will be displayed with specific colors.

  • By collections, showing alphabetically all the concepts members of a selected collection.

  • Temporal, showing all concepts/classes sorted by date of creation or modification (using dcterms properties). This feature is also available for all the semantic ressources in AgroPortal including OWL ontologies (if ontology developers provide the information of course).

  For instance, browsing the hierarchy of the main scheme in BIODIVTHES while highlighting concepts in 6 different collections with colors:

  
  
  

  
  

• Visualize SKOS-XL Labels (reified skosxl:Label objects) used to provide more information about a label. For instance “organism” in AGROVOC:

  
  
  

  
  

• For every concept, AgroPortal also computes and informs which Scheme and Collections the concepts belong to. This is trivial for Schemes (as defined in the resources by skos:inScheme property) but needs to be computed for Collections (we use the property uneskos:memberOf to encode this).

  
  
  

  This release also includes technical improvements and bug fixes such as:

• Lazy loading of classes/concepts related information (e.g., mappings) to ease and fasten the UI responsiveness;

• Use infinite scroll to list concepts in collections and list concepts by dates;

• Harmonize error messages and make them more descriptive;

• Add multiple reusables UI components or reusable Stimulus controllers.

We are also working with the OntoPortal Alliance on Dockerizing more the technology. For the moment, this release include a Docker compose for setting up AgroPortal development environment.

The full list of changes (front-end and backend) is available on the corresponding tag GitHub page. The features are backward compatible with the main OntoPortal code and we are currently working with the OntoPortal Alliance to merge back our features in the main OntoPortal code.

Release 2.3 – Oct. 2022

A few small steps towards a better mapping repository

This release include a series of improvements and refactoring with respect to how mappings between semantic resources are handled in AgroPortal. Especially, we have created the capability to load mappings described in the SSSOM format (loosing information as the OntoPortal mapping format is less expressive than SSSOM).

• We added the capacity (both via UI and API) to upload mappings in bulk from a JSON file in which mappings are represented in the « OntoPortal format »;

• This bulk load will accept a file generated by our new extension of the SSSOM python tool which transforms SSSOM mappings to OntoPortal format;

• We added an entry point to search/browse mappings per classes/concepts

  directly in the main Mapping page.

  
  
  

• We refactored how inter-portal/internal/external mappings (cf. Release 1.2) are handled and unified the edition interface for these 3 types of mappings.

  
  
  

  
  

• We now can show inside the classe/concept mappings tab the SKOS mappings explicitly defined in the semantic resource source file, aside of the other ones in the mapping repository (automatically generated e.g. SAME_URI, LOOM or uploaded by users e.g., REST). They are retrieved in the triple-store and available in both UI and API.

  
  
  

In the backend AgroPortal 2.3 also include a bunch of bug fixes, technical improvements and updates such as:

• Adopt a view component model system;

• Upgrade to Rails 7.0;

• Adopt Hotwire;

• Decrease the dependencies to Jquery/JavaScript;

• Optimized frequent SPARQL queries with attributes as list;

• Better handling of very large semantic resources files e.g., TAXREF or AGROVOC.

We also repaired and improved AgroPortal’s notification features so that users can better follow what’s going on for their selected semantic resources.

At the OntoPortal Alliance level, we are working toward re-organizing OntoPortal code around a central GitHub repository that will facilitate code sharing with the other OntoPortal installations, including BioPortal.

Release 2.2 – Feb. 2022

O’FAIRe is offered by AgroPortal: ontology FAIRness assessment at the click of the mouse

We are pleased to announce the release of AgroPortal 2.2. on Feb.2, 2022.

FAIRness assessment

This release includes the first prototype of a major new component in AgroPortal called O’FAIRe ( Ontology FAIRness assessment evaluator). O’FAIRe is a metadata-based methodology as described in [1] and [2] to automatically evaluate to which degree a semantic resource / ontology is compliant with the FAIR principles. It relies on 61 questions testing the ontology metadata or the hosting repository. O’FAIRe, implemented in AgroPortal [3], takes form in 4 different areas:

• A form on the Welcome page allows to visualize FAIRness assessment results for an ontology (or group of ontologies);

• The Browse page can sort semantic resources by FAIR scores;

• The Summary page provides details about an ontology score, showing the metadata properties used;

• The Landscape page displays details and explanations for each sub-principles.

O’FAIRe relies on the MOD1.4 metadata model to test unified metadata properties. The prototype works for any OntoPortal appliance compliant with MOD1.4. More details about O’FAIRe are available here: https://github.com/agroportal/fairness

[1] https://hal-lirmm.ccsd.cnrs.fr/lirmm-03630233

[2] https://hal-lirmm.ccsd.cnrs.fr/lirmm-03208544

[3] https://hal-lirmm.ccsd.cnrs.fr/lirmm-03630543

Ontology instances

AgroPortal now handles OWL ontology instances and displays them in the user interface. This was a long time feature request from AgroPortal/BioPortal users.

• On the Summary page, one may list all the instances in an ontology in a new tab and link back to the corresponding class in AgroPortal.

• When browsing a class, a new instance sub-tab shows the instances of this class.

• Both tabs offer a quick search by label box.

• The Browse page can now sort by classes or instance counts (or concept counts considering we have SKOS resources too).

Bug fixes and content management

• Lots of small bug fixes (admin side, server side, UI). If you notice something, please say it.

• AgroPortal now handles two default languages, English then French. It means that in the absence of @en labels in an ontology, AgroPortal will prioritize the @fr ones if they exist over the ones in other languages.

• Each time possible/relevant a pull request is made to the main NCBO code (the one used in BioPortal/OntoPortal) for sharing contributions.

• AgroPortal now hosts 139 public semantic resources and 12 private. Over the 151 resources  in AgroPortal, only 3 left are showing parsing/management issues!

• Multiple pull requests on the OntoPortal code managed by Stanford “NCBO BioPortal” group to generalize our contributions to OntoPortal.

• New user admin page.

Release 2.0 – Sept. 2020

AgroPortal 2.0 released – synchronization with OntoPortal, tons of new content and much more

We are pleased to announce the 2.0 release of the AgroPortal vocabulary and ontology repository: http://agroportal.lirmm.fr/

From a technical perspective

• AgroPortal is now based on OntoPortal 3.0. The OntoPortal Alliance is the community effort of organizations reusing the original NCBO BioPortal software.

• AgroPortal specific features (mappings, metadata model and visualization, cf. previous notes, etc.) have been merged in OntoPortal 3.0 code in our own LIRMM’s branches.

• Code developed at LIRMM for AgroPortal and the SIFR BioPortal is now hosted at: https://github.com/ontoportal-lirmm

• Side projects, community feedback, issues is still on AgroPortal’s GitHub: https://github.com/agroportal

• This release includes significantly changed user interfaces, more responsive and user friendly. We also fixed the BioMixer plugin and the graph visualization tabs are now working when browsing a class.

• For other fixes and features, you can also check BioPortal release notes. We congrat and acknowledge our collaborators at Stanford BMIR for all this work!

• AgroPortal Annotator now includes the latest version of the FastContext algorithm used to contextualize textual annotation. This feature has been mainly developed for biomedicine, but could be relevant for other contexts too.

From a community/content perspective

• AgroPortal now hosts 128 semantic resources. Many new ontologies, thesauri and other semantic resources have been uploaded in the last 3 years, either by us or directly by external users. Around half of these resources are exclusively hosted on AgroPortal.

• Fixed ontology metrics for all the semantic resources: the portal now counts 2,627,105 classes (mostly owl:Classes, not distinct) and 2,170,609 individuals (mostly skos:Concept).

• We have generated, extracted and analyzed more than 400,000 mappings between concepts based on term reuse, term overlap and declared mappings in AgroPortal ontologies (EKAW 2020 paper). Eventually such analysis will be automatically done in AgroPortal.

• We have investigated one million XRefs in 30 ontologies from the OBO world stored in AgroPortal and provided recommendations to mitigate issues (ICBO 2020 paper).

• Semantic resources include: 23 ontologies selected from the OBO Foundry registry, 30 semantic resources provided by INRAE (for which AgroPortal plays role of reference server), all the ontologies/trait dictionaries from the Crop Ontology project, and much more.

• AGROVOC is now back, sorry for the inconvenience!

Feel free to contact us for information, feedback or to upload/access agronomy related semantic resources.

Documentation: https://github.com/agroportal/documentation/wiki

Support at: agroportal-support@lirmm.fr

Report issues to: https://github.com/agroportal/documentation/issues

Release 1.4 – July 2017

Harnessing the power of metadata to visualize the landscape of agronomical ontologies

The new metadata model (release 1.3) has allowed us to implement additional features to leverage the power of metadata within the portal:

• An ontology landscape page that displays diagrams and charts about all the ontologies on the portal: http://agroportal.lirmm.fr/landscape . Please check this out and send feedback!

• A few changes to the ontology Summary page e.g., http://agroportal.lirmm.fr/ontologies/ANAEETHES

• A list of “additional metadata properties” for which, the backend values are stored with standard URIs whenever possible.

• “Get my metadata back” buttons which allow ontology developers to download the metadata that has been edited on the portal in RDF/XML, JSON-LD or N-triple syntax in order to copy/paste it in the original ontology file.

In conjunction with the PractikPharma / SIFR projects (annotation of French clinical text with ontologies) we have implemented additional features within the Annotator, including:

• Plugin-in the NegEx/ConText algorithm to detect negation or temporality for annotations. E.g. http://services.agroportal.lirmm.fr/annotator/?text=the%20plant%20show%20no%20sign%20of%20blight&ontologies=NALT&negation=true&apikey=1de0a270-29c5-4dda-b043-7c3580628cd5

• Additional output formats for the annotations (e.g.,  BRAT or Quaero corpus format)

Among the content change of this release we can mention:

• Projects from the AgBioData group

• Metadata population and curation for each ontology (feel free to send feedback or edit)

• Harmonisation of metadata fields (e.g., organization names, ontology types, languages, etc.)

• New vocabularies and ontologies such as: GACS (Global Agricultural Concept Scheme), Soy ontology, Foodie

This release includes code merge with NCBO BioPortal (5.3.0). See the release notes for more details on additionnal features: https://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes

Bug fixes of this release include:

• Multilingual synonyms are not indexed anymore

• Fix the partial parsing of big SKOS resources

• Indexation of properties (see NCBO release notes)

• Fix a few bugs in the front user interface cache

• Optimisation of metadata retrieval by ontology submission

• Automatic synchronization of groups and slices

We are pleased to announce that AgroPortal will be featured during IN-OVIVE 2017 workshop and EFITA 2017 conference’s demonstration session  in Montpellier, week of July 3rd, 2017.

Release 1.3 – April 2017

AgroPortal 1.3 (beta) released - brand new metadata model to describe ontologies

We are pleased to announce the 1.3 release of the AgroPortal: http://agroportal.lirmm.fr/

We now have an advanced prototype platform that currently hosts 64 ontologies, including 45 not present in any similar ontology repository (like NCBO BioPortal), and 8 private ontologies. We have identified 95 other candidate ontologies and we work daily to import new ones while involving/informing the original ontology developers. The platform already has around 60 registered users.

During this period, we have implemented a new metadata model to better support descriptions of ontologies and their relations, respecting recent metadata specifications, vocabularies, and practices used in the semantic web community. Then for each ontology available and uploaded in the portal, we edit and collaborate with the ontology developers to extensively describe their metadata. For a quick description of AgroPortal’s metadata project see: https://github.com/agroportal/documentation/wiki/Ontology-metadata

Among the content change of this release we can mention:

• 6 ontology groups with their specific slices. Groups associate ontologies from the same project or organization, for better identification of the provenance. For instance, http://lovinra.agroportal.lirmm.fr/ are all the vocabularies contributed by INRA.

• New important vocabularies and ontologies such as: Agrovoc, NAL thesaurus, AnaEE thesaurus, Food Ontology, 18 crop specific trait ontologies from the Crop Ontology, etc. We are working on GACS and CAB thesaurus.

• A huge amount of metadata fields populated such as for instance: http://agroportal.lirmm.fr/ontologies/NALT

• Mappings to connect to AgroLD (http://agrold.org) model

• French vocabularies or ontologies are now “view” of an empty metadata only one. E.g., http://agroportal.lirmm.fr/ontologies/CROPUSAGE . This avoid the labels in other languages to be included in search and annotator index.

The new feature of this release include:

• Better parsing of SKOS (fixed issues), we handle now big SKOS vocabularies

• We have entirely redesigned AgroPortal’s ontology submission page to facilitate editing the metadata. Whenever possible, the user interface facilitates the selection of the metadata values, while in the backend those values are stored with standard URIs

• From on ontology summary page, you can get JSON-LD link to the metadata to parse or use it with external applications

• Ontology browse page offers three additional ways to filter ontologies in the list (content, natural language, formality level) as well as three new options to sort this list. We believe these new features facilitate the process of selecting relevant ontologies.

• New features for the AgroPortal Annotator including filtering with UMLS Semantic Groups and detecting context - temporality and negation (this feature developed for clinical text is not yet evaluated for agriculture).

Release 1.2 – Sept. 2016

AgroPortal 1.2 (beta) released - an ontology portal for agronomy

We are pleased to announce the 1.2 release of the AgroPortal: http://agroportal.lirmm.fr/

AgroPortal is an ontology repository dedicated to agronomy. The platform reuses the NCBO BioPortal infrastructure and customizes it. As of today, it includes 56 ontologies (4 private ones) about multiple aspect of agricultural data: technologies, breeding, food, plant phenotypes and traits, anatomy, etc. Those ontologies have been uploaded in collaboration with several driving use cases including: INRA’s vocabularies, the Crop Ontology project, the AgroLD project, the RDA Wheat Data Interoperability WG and more recently the FAO VEST Registry.

Among the new content of this release we include:

• 18 new ontologies

• New categories for ontologies

• We have enabled specific “slice of AgroPortal” for each group of ontologies: crop, lovinra, agrold, wheat e.g.,

• http://wheat.agroportal.lirmm.fr/ allows to see/use only the ontologies selected by the RDA Wheat Data Interoperability WG;

• http://crop.agroportal.lirmm.fr/ allows to see/use only the ontologies developed within the Crop Ontology project.

Among the new feature of this release (and 1.1) we include:

• We have enabled the storing of:

• Interportal mappings: between an ontology within AgroPortal and an ontology in another portal appliance (typically the NCBO BioPortal itself).

• External mappings: between an ontology within AgroPortal and any other  ontology/vocabulary  for which URIs are available.

For instance: http://agroportal.lirmm.fr/ontologies/CO_715?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCO_715_0000165#mappings

• Multiple relation mappings i.e., the possibility to tag a mapping with multiple semantic web properties such as skos:exactMatch, gold:translation, etc.

• Annotations scoring. Annotations returned by the AgroPortal Annotator are now scored based (mainly) on frequencies. See [PDF] for details.

• Annotation RDF outputs using the Annotation Ontology. See [PDF] for details.

• A new model for ontology metadata. We have reviewed 350 properties from the most standard and relevant vocabularies out-there (21 totals) to describe metadata for ontologies (such as Dublin Core, OMV, DCAT, VOID, etc.) and selected 124 properties implemented in AgroPortal. Now, when an ontology is uploaded, metadata is directly extracted from the original file and used to populate the model. The current metadata appears on each ontology page e.g., http://agroportal.lirmm.fr/ontologies/BIOREFINERY. We are currently working on adding metadata to current ontologies and new visualization inside the portal. This work is still in progress if interested contact me.

In addition, we are pleased to announce the released of the VEST/AgroPortal unique map of standards, as the result of our collaboration with FAO within GODAN Action: http://vest.agrisemantics.org/

Every ontologies hosted in AgroPortal will automatically be included into the unique map.

AgroPortal is the result of a collaboration between: LIRMM, INRA, IRD, Bioversity International, CIRAD, FAO and the NCBO.  The project acknowledge the support of: French ANR (grant ANR-12-JS02-01001), Univ. of Montpellier, CNRS, IBC of Montpellier (grant ANR-11-BINF-0002), the NUMEV Labex (grant ANR-10-LABX-20), the EU H2020 Marie Skłodowska-Curie program (grant 701771).

Please, refer to the project with:

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé-Yeumo, Vincent Emonet, John Graybeal, Mark A. Musen, Cyril Pommier & Pierre Larmande. Reusing the NCBO BioPortal technology for agronomy to build AgroPortal, In 7th International Conference on Biomedical Ontologies, ICBO'16, Demo Session. Corvallis, Oregon, USA, August 2016. (D203), pp. 3.

Link: http://ceur-ws.org/Vol-1747/D202_ICBO2016.pdf

Please try out or contact us at agroportal-support@lirmm.fr

AgroPortal release notes: https://github.com/agroportal/documentation/wiki/Release-notes

Information: AgroPortal was presented last week at the GODAN Summit in New York City: http://summit.godan.info/

Release 1.1 – Dec. 2015

Recent activated features and/or new development includes:

• Slices enabled for crop, agrold, wheat and lovinra e.g., http://crop.agroportal.lirmm.fr/ allows to see/use only the ontologies from the Crop Ontology project.

• A specific slice shows the ontologies exclusively in AgroPortal (not in the NCBO BioPortal): http://exclu.agroportal.lirmm.fr/ (16 ontologies as of now).

• We have enabled the storing of:

• Interportal mappings: between an ontology within AgroPortal and an ontology in another portal appliance (typically the NCBO BioPortal itself).

• External mappings: between an ontology within AgroPortal and any other  ontology/vocabulary  for which URIs are available.

For instance: http://agroportal.lirmm.fr/ontologies/CO_715?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCO_715_0000165#mappings

• Multiple relation mappings i.e., the possibility to tag a mapping with multiple semantic web properties such as skos:exactMatch, gold:translation, etc.

• Annotations scoring. Score the annotation returned by the Annotator. See [PDF] for details.

• Annotation RDF outputs using AO. See [PDF] for details.

Release 1.0 beta – July 2015

AgroPortal 1.0 beta released - a portal for ontology in agronomy and plant sciences

We are pleased to announce the first release of the AgroPortal: http://agroportal.lirmm.fr/

AgroPortal is an ontology repository dedicated to the agronomic and plant domains. The platform reuses the NCBO BioPortal infrastructure and customizes it. As of today, it includes 38 ontologies which come mainly from external users, NCBO BioPortal, or driving agronomic use-cases including :

• IBC Rice Genomics & AgroLD project: rice data integration & linked RDF data from a variety of plant resources and ontologies (contact: P. Larmande)

• RDA Wheat Data Interoperability working group: a common framework for describing, representing, linking and publishing wheat data with respect to open standards (contact: E. Dzalé-Yeumo)

• INRA Linked Open Vocabularies: vocabularies produced or co-produced by INRA scientists (contacts: E. Dzalé-Yeumo & S. Aubin)

• The Crop Ontology project: a set of ontologies developed to compile validated concepts/relations on anatomy, structure and phenotype of Crops. (contacts: E. Arnaud & M-A. Laporte)

As the original BioPortal the platform enables to:

• Store ontology metadata

• Search within ontologies

• Store and retrieve mappings between ontologies

• Visualize ontology content

• Comment about ontologies, concepts and mappings

• Annotate text data with ontology concepts

• Get a recommendation about which ontology use for a text corpus or set of keywords

• Store projects which use ontologies

• And many other features!!

We are currently working on new features, that will be announced regularly.

The content of the platform is accessible via REST API and SPARQL endpoint:

http://data.agroportal.lirmm.fr/documentation

http://sparql.agroportal.lirmm.fr/test/

The  main objective of the AgroPortal project is to enable straightforward use of agronomic related ontologies, avoiding data managers and researchers the burden to deal with  complex  knowledge  engineering  issues. We want to offer a “one-stop-shop” for ontologies that will arise awareness, avoid duplicated efforts, and foster adoption of common practices. The AgroPortal  project  will specifically pay attention to respect the requirements of the agronomic/plant community. So your feedbacks are welcome!

AgroPortal is the result of a collaboration between: LIRMM, INRA, IRD, Bioversity International, CIRAD and of course the National Center for Biomedical Ontologies (NCBO) @ Stanford Univ.

The project acknowledge the support of: French ANR, Univ. of Montpellier, CNRS, IBC of Montpellier, NUMEV.

Please, refer to the project with:

Clement Jonquet, Esther Dzalé-Yeumo, Elizabeth Arnaud & Pierre Larmande. AgroPortal : a proposition for ontology-based services in the agronomic domain, In 3ème atelier INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement, IN-OVIVE'15. Rennes, France, June 2015. pp. 5. [PDF]

Please try out or contact us at agroportal-support@lirmm.fr

Information: AgroPortal was presented at the PAG meeting in San Diego January 9th and 11th (poster).