v2.4.8

What's Changed

• Fix: downloading an empty json metadata file by @syphax-bouazzouni in #283
• Fix: Erroneous slices links in home page by @SirineMhedhbi in #281
• fix: bug after search : the redirect for an empty search page and hidden popup by @SirineMhedhbi in #317
• Fix: Bug missing roots display by @SirineMhedhbi in #311
• Merge to master: Release 2.4.7 - Groups and categories administration and Bug fixes by @syphax-bouazzouni in #335

Full Changelog: v2.4.7...v2.4.8

v2.4.7

What's Changed

Metadata curator

• Refactor: Update the submission form by @syphax-bouazzouni in #136
• Feature: Metadata curator v2 by @syphax-bouazzouni in #138
• Feature: Add edit and delete submissions for users by @syphax-bouazzouni in #139
• Feature: Update the style of the mailing list section in the account page by @syphax-bouazzouni in #202

Update some page's UI design

• Feature: Update login page design by @Bilelkihal in #142
• Feature: Update lost password page design by @Bilelkihal in #143
• Feature: Update feedback design by @Bilelkihal in #156
• Feature: Update register template by @Bilelkihal in #144
• Feature: Update account page design by @Bilelkihal in #206
• Feature: Update submitted ontologies and created project sections designed by @Bilelkihal in #214

Administration application monitoring

• Feature: Add monitoring links to the admin page by @haddadzineddine in #213
• Feature: Add Newrelic configuration file by @haddadzineddine in #198
• Feature: Add newrelic production by @syphax-bouazzouni in #199

New features

• Feature: show ontology pull URL in summary page if ontology admin by @syphax-bouazzouni in #186
• Feature: Lazy load ontology submissions in summary page by @syphax-bouazzouni in #192
• Feature: Extract chips component by @Bilelkihal in #181
• Feature: Feedback page uses chips component by @Bilelkihal in #201
• Feature: Extract card message component by @Bilelkihal in #166

Reduce technical debt and code refactoring

• Feature: Migrate notes to Hotwire by @syphax-bouazzouni in #177
• Feature: Create subscribe to ontology button component by @syphax-bouazzouni in #175
• Feature: Migrate the fair score details popup from Jquery Facebox to Turbo modal by @syphax-bouazzouni in #176

Bugs fixes

• Fix: Add user to the mailing list on signup by @haddadzineddine in #132
• Fix: browse search length problem by @Bilelkihal in #119
• Fix: Enable widgets and Biomixer by @syphax-bouazzouni in #145
• Fix: add db volume to dockerfile by @haddadzineddine in #149
• Fix: widgets JS by @syphax-bouazzouni in #150
• Fix: response_errors to use response body by @syphax-bouazzouni in #152
• Fix: Submission creation and error handling by @syphax-bouazzouni in #155
• Fix: error messages on ontology creation by @syphax-bouazzouni in #158
• Fix: class jump to by @syphax-bouazzouni in #159
• Fix: response error handling for projects and users by @syphax-bouazzouni in #160
• Fix: Force cast to string submission version of type number by @syphax-bouazzouni in #163
• Fix: Admin ontology process success message by @syphax-bouazzouni in #164
• Fix: add a user to the mailing list on signup by @haddadzineddine in #148
• Fix: Trigger browser reload on summary page links clicks by @syphax-bouazzouni in #173
• Fix: some bugs on browser back click by @syphax-bouazzouni in #174
• Fix: Switch component to have a boolean version for submissions form by @syphax-bouazzouni in #182
• Fix: input attribute of type uri getting only the first letter (e.g h) and saving local:h by @syphax-bouazzouni in #183
• Fix: included in data catalog not showing the right name in the button by @syphax-bouazzouni in #184
• Fix: add display=all parameter to access concept json link by @syphax-bouazzouni in #185
• Fix: Remove the option None for all the submissions from select attributes by @syphax-bouazzouni in #187
• Fix: Password recovery success message by @Bilelkihal in #197
• Fix: Production colors issues by @Bilelkihal in #205
• Fix: Account page subscription mail by @Bilelkihal in #208
• Fix: Signup page input fields validation by @Bilelkihal in #212
• Fix: to rescue fairness service if is unreachable by @syphax-bouazzouni in #218
• Fix: disable cache_refresh_all for submission save by @syphax-bouazzouni in #221
• Fix: Admin errors response handling by @syphax-bouazzouni in #229

Full Changelog: v2.4.0...v2.4.7

v2.4.0

Features

• Add SKOS features

  • Collections (show, show_label, show_members) (6ddf30b)

  • SKOS XL label (show and show_label) (138cc1a)

  • Schemes (show, show_label) (b900498)

• Add three types of browsers for concepts

  • Tree view, with scheme and collection filters (95fe424)

  • List view, with collection filter and infinite scroll (4ec1e6b)

  • Date view, with infinite scroll (b04c391)

• Update concepts show_label to use Ajax label button UI component (bfc800d)

• Update concepts details by showing concept type, memberOf, and inScheme attributes

• Make mapping lazy loaded (loaded in the background after page display) (363819c)

• Harmonize error messages and make them more descriptive (bf11e85)

• Merge to upstream v6.9.0 (3c3065f)

  • Capistrano depolyment
  • Linear gradient fix (ncbo#218)
  • Add synonyms change request (ncbo#234)
  • Clean configuration sample from no more used variables

Bugs

• Submission update does not redirect to ontology page (#134)
• Ontology update page does not redirect to the ontology page (#97)

Technical

• Add reusable UI component

  • Ajax label button (36e4df9)
  • Concept (class, scheme, collection, ...) details UI component, with two divided sections, the mapped attributes first and then the others properties (4440a89)
  • Infinite scroll UI component (f33a6ee)
  • Turbo frame component (with loading, success, and error states) (64ffba5, b814495)

• Add reusable Stimulus controllers (reusable js code)

  • Chosen controller: to use JQuery chosen (fea55dd)
  • Splitter controller: to use Split.js (to divide a container into two resizable sections, e.g classes details with the tree view in the left side) (f5267b0)
  • History controller: to use Histroy.js to update the URL or the page state (432001f)
  • Tree view controller: to use Jquery tree (7ad7c29)
  • Tooltip controller: use toolipster.js to add a tooltip on text hover (0c3247a)
  • Turbo frame controller: to update turbo frame on demand with JS

• Add reusable partials

  • Collections picker (6691d84)
  • Scheme picker (f822d50)
  • Jump to concepts with filters button (7053f5a)

• Add docker development environment (654314b)

Backend changes

• https://github.com/ontoportal-lirmm/ontologies_linked_data/releases/tag/v2.4.0
• https://github.com/ontoportal-lirmm/ontologies_api/releases/tag/v2.3.0
• https://github.com/ontoportal-lirmm/goo/releases/tag/v2.3.0

v2.3.0

Changes

Features

• Add bulk load mapping with a JSON file (agroportal/project-management#292)
• Show ontology internal mappings (skos:exactMatch, ...) (agroportal/project-management#302)
• Update the UI of the mappings (agroportal/project-management#299)
  • Merge new mapping and the new external mapping forms
  • Add mapping edition
  • Add search mapping by a class
  • Style mappings page

Bugs

• Hide fairness module for AGROVOC (#79)
• Fix the local:local text in some fields of the submission form (ontoportal-lirmm/ontologies_linked_data#40)

Technical

• Update to Rails 7 (ncbo#201)
• Refactor the ontology-viewer to replace the old js with Hotwire (agroportal/project-management#303)
• Add view-component system (ncbo#224)
• Merge to 'upstream' v6.7.1 (19c1d0d)

Backend changes

• https://github.com/ontoportal-lirmm/ontologies_linked_data/releases/tag/v2.3.0
• https://github.com/ontoportal-lirmm/ontologies_api/releases/tag/v2.2.0
• https://github.com/ontoportal-lirmm/goo/releases/tag/v2.2.0

Full Changelog: v2.2.3...v2.3.1

v2.2.3

• v2.0.1: Merge with NCBO (#12)
• v2.0.2: Update browse page badges (agroportal/project-management#182)
• v2.1.0: Add instances feature (agroportal/project-management#165)
• v2.1.4: update robotos file (#59)
• v2.1.5: Print modification date in summary dans la page of an ontologie (#30)
• v2.2.0: Adding the O’FAIRE: Ontology FAIRness Evaluator module (agroportal/project-management#152)
• v2.2.1: FAIRness Evaluator module fixes :
  - make the FAIRness view in the home page responsive
  - Use the apikey of the user if logged
  - Show the FAIR score of privates ontologies if the user owned it or is admin
• v2.2.2: FAIRness Evaluator module fixes :
  - Print the FAIR score in the browse page even if the ontologie has no metrics
  - Fixing the problem of printing floating numbers
  - Fixing the problem of the button “Go” of the admin page
• v2.2.3: Instances feature fixes :
  - Refactor the code to use web component and rails partials

v2.0.0

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: [email protected]

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

Acknowledgments:

AgroPortal is currently being developed within French ANR D2KAB project (ANR-18-CE23-0017). It also receives or received support from ANR SIFR project (ANR-12-JS02-0010), European Union H2020-MSCA SIFRm project (No 701771), the NUMEV Labex (ANR-10-LABX-0020), the IBC of Montpellier project (ANR-11-BINF0002), the Agro Labex (ANR-10-LABX-0001) as well as from University of Montpellier, CNRS and INRAE.