diff --git a/app/assets/images/logos/ontoportal.svg b/app/assets/images/logos/ontoportal.svg new file mode 100644 index 000000000..dfb0838d3 --- /dev/null +++ b/app/assets/images/logos/ontoportal.svg @@ -0,0 +1,3 @@ + + + diff --git a/app/assets/images/social/github.svg b/app/assets/images/social/github.svg new file mode 100644 index 000000000..9f2ef1737 --- /dev/null +++ b/app/assets/images/social/github.svg @@ -0,0 +1,3 @@ + + + \ No newline at end of file diff --git a/app/assets/images/social/people.svg b/app/assets/images/social/people.svg new file mode 100644 index 000000000..85f1d5fd0 --- /dev/null +++ b/app/assets/images/social/people.svg @@ -0,0 +1,3 @@ + + + \ No newline at end of file diff --git a/app/assets/images/social/twitter.svg b/app/assets/images/social/twitter.svg new file mode 100644 index 000000000..162e21ae2 --- /dev/null +++ b/app/assets/images/social/twitter.svg @@ -0,0 +1,10 @@ + + + + + + + + + + \ No newline at end of file diff --git a/app/assets/stylesheets/footer.scss b/app/assets/stylesheets/footer.scss index 927971394..dec58f53f 100644 --- a/app/assets/stylesheets/footer.scss +++ b/app/assets/stylesheets/footer.scss @@ -1,3 +1,55 @@ -.legal-text { - font-size: 0.9rem; -} \ No newline at end of file +.footer-container{ + display: flex; + justify-content: center; + background-color: var(--primary-color); +} +footer{ + width: 1280px; + background-color: var(--primary-color); + padding: 40px 100px; +} + +.footer-header{ + display: flex; + justify-content: space-between; + margin-bottom: 40px; +} +.footer-logo{ + color: white; + display: flex; + align-items: center; +} +.footer-logo p{ + margin-bottom: 0; + font-weight: 700; + font-size: 18px; + margin-left: 20px; +} +.footer-social-media-links a{ + margin-left: 20px; +} +.footer-nav-links{ + display: flex; + flex-wrap: wrap; + justify-content: space-between; +} +.footer-nav-links div h2{ + font-size: 21px; + font-weight: 700; + color: white; + margin-bottom: 10px; +} +.footer-nav-links div div{ + display:flex; + flex-direction: column; +} +.footer-nav-links div a{ + font-size: 16px; + font-weight: 400; + color: white !important; + margin-bottom: 10px; + opacity: 60%; +} +.footer-nav-links div a:hover{ + opacity: 100%; +} diff --git a/app/assets/stylesheets/themes/lirmm/main.scss b/app/assets/stylesheets/themes/lirmm/main.scss index e50dcf48d..d5bb078c1 100644 --- a/app/assets/stylesheets/themes/lirmm/main.scss +++ b/app/assets/stylesheets/themes/lirmm/main.scss @@ -241,22 +241,3 @@ div.logos a { } } -/************************************ - * FOOTER -************************************/ -footer, .footer { - background-color: $color-secondary !important; - position: relative !important; -} - -footer img { - height: 32px; -} - -footer a.logo.connect img { - margin-right: 10px; -} - -.legal-text { - font-size: 0.9rem; -} diff --git a/app/views/annotator/index.html.haml b/app/views/annotator/index.html.haml index 6c12a1f55..ca9fa67bb 100644 --- a/app/views/annotator/index.html.haml +++ b/app/views/annotator/index.html.haml @@ -3,7 +3,7 @@ %head = javascript_include_tag "bp_annotator" -%div.container-fluid +%div.container-fluid.flex-grow-1 %div.row %div.col %h2.mt-3 Annotator diff --git a/app/views/annotatorplus/index.html.haml b/app/views/annotatorplus/index.html.haml index 0fab2ce09..01cbdbbac 100644 --- a/app/views/annotatorplus/index.html.haml +++ b/app/views/annotatorplus/index.html.haml @@ -3,7 +3,7 @@ %head = javascript_include_tag "bp_annotatorplus" -%div.container-fluid +%div.container-fluid.flex-grow-1 %div.row %div.col %h2.mt-3 Annotator + diff --git a/app/views/layouts/_footer.html.haml b/app/views/layouts/_footer.html.haml index a88f4166f..2cdd9b7c0 100644 --- a/app/views/layouts/_footer.html.haml +++ b/app/views/layouts/_footer.html.haml @@ -1,33 +1,32 @@ -%footer.footer.pt-4.mt-5 - %div.container - %div.row - - $FOOTER_LINKS.to_h[:top].to_a.each do |footer_links_block| - %div.col-6.col-md - %h6= footer_links_block[:column_header] - %ul.list-unstyled - - footer_links_block[:links].each do |footer_links_row| - %li - - footer_links_row.each do |footer_link| - = render_footer_link footer_link - %div.row.legal-text - %div.col - = t('.grant_html', site: $SITE) - %div.row.pt-2 - - $FOOTER_LINKS.to_h[:bottom].to_a.each do |footer_links_block| - %div.col-6.col-md - - if footer_links_block[:column_header].present? - %h6= footer_links_block[:column_header] - %ul.list-inline - - footer_links_block[:links].each do |footer_links_row| - - footer_links_row.each_with_index do |footer_link, i| - %li.list-inline-item - = render_footer_link footer_link - - unless i >= footer_links_row.size - 1 - %li.list-inline-item - = raw(footer_links_block[:separator]) +%br +%br/ +.footer-container + %footer + .footer-header + .footer-logo + %img{:src => "#{asset_path("logos/ontoportal.svg")}"} + - logo = $UI_THEME.to_s.capitalize + - logo.sub! 'portal' , 'Portal' + %p + = logo + .footer-social-media-links + - $FOOTER_LINKS[:social].each do |link| + %a{:href => link[:link], :target => "_blank"} + %img{:src => "#{asset_path(link[:logo])}"}/ + .footer-nav-links + - $FOOTER_LINKS[:sections].each do |key, section_links| + %div + %h2 + = t("layout.footer."+key.to_s) + %div + - section_links.each do |section , link| + %a{:href => link, :target => "_blank"} + = t("layout.footer."+section.to_s) + + = javascript_include_tag "application" diff --git a/app/views/layouts/_header.html.erb b/app/views/layouts/_header.html.erb index 730a85af5..0530d3209 100644 --- a/app/views/layouts/_header.html.erb +++ b/app/views/layouts/_header.html.erb @@ -43,5 +43,5 @@ <%=render partial: 'layouts/topnav'%> -
+
<%=render partial: 'layouts/notices'%> \ No newline at end of file diff --git a/app/views/layouts/appliance.html.haml b/app/views/layouts/appliance.html.haml index aae2cc1d6..9bf582dbb 100644 --- a/app/views/layouts/appliance.html.haml +++ b/app/views/layouts/appliance.html.haml @@ -28,7 +28,7 @@ %body{:class => "#{controller_name} #{action_name}"} = render partial: "layouts/topnav" - %div.container-fluid + %div.container-fluid.flex-grow-1 = render partial: "layouts/notices" = render TurboModalComponent.new(id: 'application_modal') = yield diff --git a/app/views/mappings/index.html.haml b/app/views/mappings/index.html.haml index 438f3658f..94807c194 100644 --- a/app/views/mappings/index.html.haml +++ b/app/views/mappings/index.html.haml @@ -1,5 +1,5 @@ - @title = "Mappings" -%div#mappings_container.container-fluid.py-4 +%div#mappings_container.container-fluid.py-4.flex-grow-1 %h1.my-1 Mappings %div#mappings_uploader.my-2 diff --git a/app/views/ncbo_annotatorplus/index.html.haml b/app/views/ncbo_annotatorplus/index.html.haml index ba1315f02..9d9cffc47 100644 --- a/app/views/ncbo_annotatorplus/index.html.haml +++ b/app/views/ncbo_annotatorplus/index.html.haml @@ -3,7 +3,7 @@ %head = javascript_include_tag "bp_annotator" -%div.container-fluid.annotator +%div.container-fluid.annotator.flex-grow-1 %div.row %div.col %h2.mt-3 NCBO Annotator + diff --git a/config/locales/en.yml b/config/locales/en.yml index b37ebbb55..1af0c436b 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -1,66 +1,9 @@ en: - - about: > -
-

Abstract

-

- Many vocabularies and ontologies are produced to represent and annotate agronomic data. Therefore, there is a need of - a common platform to identify, host and use them in agro-informatics application. The AgroPortal project aims to offer - a reference ontology repository for agronomy, reusing the NCBO BioPortal technology. The scientific outcomes and the - experience of the biomedical domain are thus exploited and transposed in the agronomy domain, including plants, food, - environment and possibly animal sciences. We offer an ontology portal which features ontology hosting, search, versioning, - visualization, comment, recommendation, enables semantic annotation, as well as storing and exploiting ontology alignments. - All of these within a fully semantic web compliant infrastructure. The AgroPortal specifically pays attention to respect the - requirements of the agronomic community in terms of ontology formats (e.g., SKOS, trait dictionaries) or supported features. - AgroPortal project is based on five driving agronomic use cases which participate in the design and orientation of the platform. - AgroPortal already offers a robust and stable reference repository highly valuable for the agronomic domain. -

-

Use cases

- -
-

New features

-

- See the release notes -

-
-

Partners

-

The National Center For Biomedical Ontology (NCBO), Institut de Recherche pour le Développement (IRD), Research Data Alliance (RDA), - Bioversity International, Food & Agriculture Organization (FAO), Global Open Data for Agriculture & Nutrition (Godan Action), Institut National de la Recherche Agronomique (INRA)

-

Acknowledgments

-

The AgroPortal is partly achieved within the Semantic Indexing of French biomedical Resources (SIFR) project - that received funding from the EU H2020 research and innovation programme under the Marie Sklodowska-Curie (grant 701771) - and the French National Research Agency (grant ANR-12-JS02-01001), the NUMEV Labex (grant ANR-10-LABX-20), - the Computational Biology Institute of Montpellier (grant ANR-11-BINF-0002) as well as by University of Montpellier and the CNRS. - We also thank the National Center for Biomedical Ontologies for help and time spent with us in deploying the AgroPortal.

-

Team

- To contact us: firstname.lastname@lirmm.fr -
    -
  • Clément Jonquet, researcher at LIRMM (Univ. of Montpellier, France), main investigator of the AgroPortal project
  • -
  • Anne Toulet, researcher at LIRMM (Univ. of Montpellier, France)
  • -
  • Vincent Emonet, engineer at LIRMM (Univ. of Montpellier, France)
  • -
-
- - activerecord: - errors: - models: - license: - attributes: - encrypted_key: - invalid_license_key: is an invalid license key - no_appliance_id_for_comparison: couldn't be validated. Unable to retrieve virtual appliance ID. - appliance_id_mismatch: is an appliance ID mismatch - - admin: - licenses: - create: - success: License successfully renewed! + nbco_annotatosplus: + score_help: "Score annotations following previous NCBO 2009 measure (old) or Score annotations following C-Value measure (cvalue) or Score annotations following C-Value measure with hierarchy expansion (cvalueh)" + start_typing_to_select: "Start typing to select %{type} or leave blank to use all" + include_ancestors_up_to_level: "Include ancestors up to level" + include_score: "Include score" date: formats: @@ -116,7 +59,48 @@ en: tooltip: "Enable FastContext to detect : if a concept has been negated (affirmed, negated), who experienced the found concept (patient, other), when the annotated concept occurred (recent, historical, hypothetical), and/or if the annotated concept is uncertain (certain, uncertain)." sample_text: Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye. - nbco_annotatosplus: + select: "Select %{name}" + + fast_context: + title: "FastContext" + help: "Activate FastContext to detect: if a concept has been negated (affirmed, negated), who experienced the concept found (patient, other), when the annotated concept occurred (recent, historical, hypothetical), and/or if the annotated concept is uncertain (certain, uncertain)." + + annotations: "Annotations" + + filters: + by: + filter: "Filter" + title: "Results are filtered by" + class: "Class" + ontology: "Ontology" + match_type: "Type" + match_context: "Context" + matched_class: "Associated Class" + matched_ontology: "Associated Ontology" + umls_sem_type: "UMLS Semantic Type" + score: "Score" + negation: "Negation" + experiencer: "Experiencer" + temporality: "Temporality" + certainty: "Certainty" + + additional_parameters_explained_at: "Additional parameters are explained on the page:" + format_results_as: "Format results as:" + reproduce_results_using: "Reproduce these results using the" + match_longest_only: "Match longest only" + match_partial_words: "Recognize partial words" + include_mappings: "Include mappings" + exclude_numbers: "Exclude numbers" + exclude_synonyms: "Exclude synonyms" + max_hierarchy_level: "Include ancestors up to level" + score: "Include score" + score_help: "Score annotations according to the previous NCBO 2009 measure (old) or score annotations using the C-Value measure (cvalue) or score annotations using the C-Value measure with hierarchy expansion (cvalueh)" + score_threshold: "Filter by score threshold" + score_threshold_help: "Specify the minimum score value for annotations" + confidence_threshold: "Filter confidence threshold" + confidence_threshold_help: "Specify the minimum position in the scores distribution (between 1 and 100)" + entity_recognizer: "entity recognition tool" + index: intro: > The NCBO Annotator+ is a proxy calling the NCBO Annotator Web service on the NCBO BioPortal. @@ -144,28 +128,425 @@ en: index: intro: Browse a selection of projects that use %{site} resources + landscape: + title: "%{site} Landscape" + intro: Visualize data retrieved from ontologies stored in the portal + groups_and_categories: Groups and Categories + ontologies_by: "Ontologies by %{type}" + ontologies_count_by_catalog: Number of ontologies in each data catalog + properties_use: Property Usage + properties_usage_proportion: The proportion of properties usage among stored ontologies + ontologies_languages: Natural languages of ontologies + ontologies_licenses: Licenses used by ontologies + ontology_tools: Most used tools to build ontologies + more_properties_charts: More properties charts + ontology_properties_pie_charts: Pie charts for the properties used in ontologies + owl_ontology_preflabel_uris: URIs for prefLabel properties used for OWL ontologies + owl_ontology_synonym_uris: URIs for synonym properties used for OWL ontologies + owl_ontology_definition_uris: URIs for definition properties used for OWL ontologies + owl_ontology_author_uris: URIs for author properties used for OWL ontologies + ontology_types: Ontology types + ontology_formality_levels: Formality levels of ontologies + ontologies_formats: Format used + ontologies_contributors: Contributors to ontology development + most_active_people: Most active people + most_mentioned_people: Most mentioned people as contact, creator, contributor or curator + most_active_organizations: Most active organizations + funding_endorsing_organizations: Organizations funding and endorsing the most ontologies + ontologies_activity_on: "Ontology Activity on %{site}" + most_active_people_as_reviewer: "Most active people as reviewers" + most_mentioned_people_as_reviewer: People who published notes, reviews, and projects + most_active_ontologies: "Most active ontologies" + ontologies_with_notes_reviews_projects: "Ontologies with notes, reviews, and projects" + ontology_relations_network: "Ontology Relations Network" + relations_between_stored_ontologies: "Relations between stored ontologies in the portal" + filter_network: "Filter network" + ontology_fairness_evaluator: "Ontology FAIRness Evaluator (O’FAIRe)" + average_metrics: "Average metrics" + group: Group + category: Category + size: Size + + home: + find_ontology: "Find an ontology" + search_class: "Search Class" + browse_by_group: "Browse by Group" + browse_ontologies: "Browse ontologies" + comprehensive_repository: "the most comprehensive repository of biomedical ontologies in the world" + advanced_search: "Advanced Search" + ontology_visits: "Ontology visits" + fair_scores: "FAIR Scores" + clear_selection: "Clear Selection" + latest_notes: "Latest Notes" + ontologies: "Ontologies" + classes: "Classes" + individuals: "People" + projects: "Projects" + users: "Users" + no_recent_notes: "No recent notes were submitted" + index: + find_ontology_placeholder: Start typing the ontology name, then choose from + query_placeholder: Enter a class, eg Melanoma + tagline: the world's most comprehensive repository of biomedical ontologies + title: Welcome to the %{organization} + welcome: Welcome to the %{site}, + help: + welcome: Welcome to the %{site} of the National Center for Biomedical Ontology. %{site} is a web application for accessing and sharing biomedical ontologies. + getting_started: > + %{site} allows users to browse, upload, download, search, comment, and create mappings for ontologies. + browse: > + Users can browse and explore individual ontologies by navigating either in a tree structure or in an animated graphical view. Users can also view mappings and + ontology metadata and ontology download. Additionally, logged in users can submit a new ontology to the library. + rest_examples_html: View documentation and examples for the %{site} REST API. + announce_list_html: > + To receive notices of new releases or site outages, please subscribe to + bioontology support list. + + recommend: + intro: Get recommendations for the most relevant ontologies from an excerpt of a biomedical text or a list of keywords + title: "recommender" + ontology_recommender: "Ontology Recommender" + ontology_recommendation_input: "Please paste a paragraph of text or some keywords to compute ontology recommendations." + weight_sum_greater_than_zero: "The sum of weights must be greater than zero" + weights_greater_than_zero: "All weights must be greater than or equal to zero" + valid_numeric_weights: "All weights must be valid numeric values" + valid_integer_max_ontologies_per_set: "Max ontologies per set must be a valid integer value" + valid_max_ontologies_per_set_range: "Max ontologies per set must be a number between 2 and 4" + recommendation_error: "Problem retrieving recommendations, please try again" + no_recommendations: "No recommendations found" + no_sets_recommended: "There are no recommended ontology sets for the provided input. Please try the 'Ontologies' output." + text_length_limit: "Please use less than 500 words. If you need to annotate longer pieces of text, you can use the recommendation web service." + + mappings: + title: "Correspondences" + upload_mappings: "Upload mappings" + mappings_bulk_load: "Mapping Bulk Load" + intro: "Browse mappings between classes of different ontologies" + no_mappings_available: "No mappings available" + loading_mappings: "Loading mappings..." + find_mappings: "Find mappings of a class/concept" + view_mappings_help: "View mappings help" + select_class: "Start typing to select a class" + select_ontologies: "Start typing to select ontologies or leave blank to use all ontologies" + select_semantic_types: "Select UMLS semantic types" + select_semantic_types_help: "Start typing to select UMLS semantic types or leave blank to use all types" + select_semantic_groups: "Select UMLS semantic groups" + select_semantic_groups_help: "Start typing to select UMLS semantic groups or leave blank to use all groups" + include_ancestors_up_to_level: "Include ancestors up to level" + include_score: "Include score" + + annotator: + title: "Annotator" + get_annotator: "Get annotations" + filters: + match_longest_only: "Match longest only" + match_partial_words: "Recognize partial words" + include_mappings: "Include Mappings" + exclude_numbers: "Exclude Numbers" + exclude_synonyms: "Exclude synonyms" + max_hierarchy_level: "Include ancestors up to level" + score: "Include score" + score_help: "Score annotations following previous NCBO 2009 measure (old) or Score annotations following C-Value measure (cvalue) or Score annotations following C-Value measure with hierarchy expansion (cvalueh)" + score_threshold: "Filter by score threshold" + score_threshold_help: "Specify minimum score value for annotations" + confidence_threshold: "Filter Confidence Threshold" + confidence_threshold_help: "Specify the minimum position in the score distribution (between 1 and 100)" + recognizer recognizer: "entity recognition tool" + start_typing_to_select: "Start typing to select %{type} or leave blank to use all" + select: "Select %{name}" + enter_or_paste_text: "Enter or paste text to annotate" + fast_context: "FastContext" + lemmatize: "Lemmatize" + annotations_result: "Annotations" + results_filtered_by: "Results are filtered by" + + umls: + semantic_types: "UMLS Semantic Types" + semantic_groups: "UMLS Semantic Groups" + index: + intro: Get annotations for biomedical text with ontology classes + annotatorplus_html: Check out the beta version of AnnotatorPlus; a new version of the Annotator with added support for negation, and more! + fast_context: + tooltip: "Enable FastContext to detect: if a concept was denied (affirmed, denied), who experienced the found concept (patient, other), when the annotated concept occurred (recent, historical, hypothetical), and/ or if the annotated concept is uncertain (certain, uncertain)." + lemmatize: + tooltip: "Enable Lemmatize to lemmatize submitted text and use a lemmatized dictionary for annotations" + sample_text: Melanoma is a malignant tumor of melanocytes found mainly in the skin but also in the intestine and the eye. + + ontology_details: + metadata: + details: "Details" + acronym: "Acronym" + visibility: "Visibility" + viewing_restriction: "Viewing Restriction" + view_of_ontology: "View of ontology" + description: "Description" + status: "Status" + format: "Format" + contact: "Contact" + categories: "Categories" + groups: "Groups" + pull_url: "Pull URL" + submissions: "Submissions" + links: "Links" + add_submission: "Add Submission" + views_of: "Views of" + create_new_view: "Create a new view" + no_views_of: "No views of %{name} available" + go_to_rest_api_json_entry: "Go to REST API JSON Entry" + get_my_metadata_back: "Get my metadata back" + n_triple: "N-Triple" + json_ld: "JSON-LD" + rdf_xml: "RDF/XML" + view_individual_metrics_definitions: "View individual metrics definitions" + metrics: "Metrics" + metrics_not_calculated_yet: "We have not yet calculated metrics for" + classes: "Classes" + individuals: "Individuals" + properties: "Properties" + max_depth: "Maximum depth" + max_children: "Maximum number of children" + avg_children: "Average number of children" + single_child_classes: "Classes with a single child" + many_children_classes: "Classes with more than 25 children" + no_definition_classes: "Classes without definition" + visits: "Visits" + download_as_csv: "Download as CSV" + projects_using: "Projects Using" + no_projects_using: "No projects are using" + create_new_project: "Create a new project" + additional_metadata: "Additional Metadata" + + layout: + header: + browse: "Browse" + search: "Search" + mappings: "Mappings" + recommend: "Recommend" + annotator: "Annotator" + ncbo_annotator_plus: "NCBO Annotator+" + projects: "Projects" + landscape: "Landscape" + login: "Login" + account_setting: "Account Settings" + submit_feedback: "Send Feedback" + help: "Help" + release_notes: "Release Notes" + publications: "Publications" + footer: + products: Products + ontoportal: OntoPortal + release_notes: Release Notes + api: API + sparql: SPARQL + support: Support + contact_us: Contact Us + wiki: Wiki + documentation: Documentation + agreements: Agreements + terms: Terms + privacy_policy: Privacy Policy + cite_us: Cite Us + acknowledgments: Acknowledgments + about: About + about_us: About Us + projects: Projects + team: Team + copyright_html: Copyright © 2005-2022, Leland Stanford Junior University Board of Trustees. All rights reserved. + grant_html: > + %{site} is currently being developed as part of the ANR D2KAB project (ANR-18-CE23-0017). It receives or has also received support from the ANR SIFR project (ANR-12-JS02-0010), European Union Project H2020-MSCA SIFRm (N° 701771), the Labex NUMEV (ANR-10-LABX-20), the Montpellier IBC project (ANR-11 -BINF0002) , the Agro Labex (ANR-10-LABX-0001) as well than the University of Montpellier and the CNRS. + notes: + license_contact: > + For more information, email support@ontoportal.org or + visit https://ontoportal.org/licensing. + license_obtain: > + If you are the owner of this OntoPortal installation, you can visit + https://license.ontoportal.org to obtain a license. + license_expired: > + We're sorry, but the license for this OntoPortal installation has expired. If you are the owner of this OntoPortal installation, + please visit https://license.ontoportal.org to renew your license. + license_trial: + one: This OntoPortal appliance installation is a trial license, which will expire in 1 day. + other: This OntoPortal appliance installation is a trial license, which will expire in %{count} days. + # Other + + about: > +
+

Summary

+

+ Many vocabularies and ontologies are produced to represent and annotate agronomic data. It is therefore necessary to have a common platform to identify them, host them and use them in agro-informatics applications. The AgroPortal project aims to provide a repository of reference ontologies for agronomy, by reusing the NCBO BioPortal technology. The scientific results and the experience of the biomedical field are thus exploited and transposed in the field of agronomy, including plants, food, the environment and possibly animal sciences. We propose an ontology portal that offers ontology hosting, search, versioning, visualization, commenting, recommendation, allows semantic annotation, as well as storing and exploiting alignments of ontologies. All this in an infrastructure fully compliant with the Semantic Web. The AgroPortal project pays particular attention to meeting the requirements of the agronomic community in terms of ontology formats (e.g. SKOS, trait dictionaries) or supported functionalities. The AgroPortal project is based on five agronomic use cases that participate in the design and orientation of the platform. AgroPortal already offers a robust and stable reference repository, of great value for the field of agronomy. +

+

Use cases

+ +
+

New Features

+

+ See the release-notes +

+
+

Partners

+

The National Center for Biomedical Ontology (NCBO), the Research Institute for Development (IRD), Research Data Alliance (RDA), + Bioversity International, Food & Agriculture Organization (FAO), Global Open Data for Agriculture & Nutrition (Godan Action), National Institute for Agronomic Research (INRA)

+

thanks

+

The AgroPortail is partly produced as part of the Semantic Indexing of French Biomedical Resources project (SIFR) + who have received funding from the EU H2020 research and innovation program under Marie Sklodowska-Curie (grant 701771) + and the National Research Agency (ANR-12-JS02-01001 grant), Labex NUMEV (ANR-10-LABX-20 grant), + the Institute of Computational Biology of Montpellier (grant ANR-11-BINF-0002) as well as by the University of Montpellier and the CNRS. + We also thank the National Center of Biomedical Ontologies for their help and the time spent with us in the deployment of the AgroPortail.

+

Team

+ To contact us: firstname.lastname@lirmm.fr +
    +
  • Clément Jonquet, researcher at LIRMM (Univ. of Montpellier, France), principal investigator of the AgroPortal project
  • +
  • Anne Toulet, researcher at LIRMM (Univ. of Montpellier, France)
  • +
  • Vincent Emonet, engineer at LIRMM (Univ. of Montpellier, France)
  • +
+
+ + activaterecord: + errors: + models: + license: + attributes: + encrypted_key: + invalid_license_key: is an invalid license key + no_appliance_id_for_comparison: Could not be validated. Unable to retrieve virtual appliance ID. + appliance_id_mismatch: is an appliance id mismatch + + admin: + licenses: + create: + success: License renewed successfully! + + date: + formats: + year_month_day_concise: "%Y-%m-%d" # 2017-03-01 + month_day_year: "%b %-d, %Y" # Mar 1, 2017 + monthfull_day_year: "%B %-d, %Y" # March 1, 2017 + ontologies: - intro: Browse the library of ontologies + self: "Ontologies" + loading: Loading ontologies + intro: Browse the Ontology Library + please_wait: Please wait.. + browse: Explore + welcome_admin: Welcome admin + admin_help: This color indicates features reserved for administrators + debug_info: Debug Info + submit_new_ontology: Submit a new ontology + entry_type: Entry Type + uploaded_in_the_last: Uploaded in the last concepts: request_term: new_term_instructions: > -

This ontology integrates with OntoloBridge, allowing community users to suggest additions to the public ontology. Complete the template below to submit a term request directly to the ontology maintainer.

-
-

Term Label (required)
Suggested term name. If a term can be described with multiple synonyms, only list the preferred name here.

-
-
-

Term description (required)
A brief definition, description, or usage of your suggested term. Additional term synonyms may be listed in this section.

-
-
-

Superclass (required)
The parent term of the suggested term. The parent term should be an existing entry of the current ontology. The superclass can be selected directly from Bioportal's Classes tree viewer.

-
-
-

References (optional)
Provide evidence for the existence of the requested term such as Pubmed IDs of papers or links to other resources that describe the term.

-
-
-

Justification (optional)
Provide any additional information about the requested term here.

-
- mappings: - intro: Browse mappings between classes in different ontologies +

This ontology integrates with OntoloBridge, allowing community users to suggest additions to the public ontology. Complete the template below to submit a term request directly to the Ontology Manager.

+
+

Term label (required)
Suggested term name. If a term can be described with more than one synonym, enter only the preferred name here.

+
+
+

Term Description (required)
A brief definition, description, or usage of the suggested term. Synonyms of additional terms may be listed in this section.

+
+
+

Superclass (required)
The parent term of the suggested term. The parent term must be an existing entry in the current ontology. The superclass can be selected directly from the Bioportal class tree.

+
+
+

References (optional)
Provide evidence that the requested term exists, such as Pubmed IDs of articles or links to other resources describing the term.

+
+
+

Justification (optional)
Provide here any additional information about the requested term.

+
+ + # General + + showing: Display + of: of + sort: Sort + popular: Popular + name: Name + classes_count: Number of classes + instances_concepts_count: Number of instances/concepts + Notes: Notes + upload_date: Upload date + release_date: Release date + fair_score: FAIR score + search_rank: Search Rank + no_matches: No matches! + uploaded: Uploaded + view_of: View of + view: View + summary_only: Summary only + groups: Groups + categories: Categories + admins: Administrators + status: Status + no_submissions_available: No submissions available + classes: classes + category: Category + group: Group + size: size + ontology_content: Ontology content + natural_language: Natural language + formality_levels: Formality levels + is_of_type: Is of type + missing_status: Missing Status + types: Types + artifacts: Artifacts + formats: formats + selected_ontologies: Selected ontologies + all: "All" + none: "none" + keywords: "Keywords" + keywords_separated_by_commas: "Keywords separated by commas" + see_details: "See details" + view_fair_scores_definitions: "View fair scores definitions" + get_json_version: "Get the json version" + select_ontologies: "Start typing to select ontologies or leave blank to use them all" + clear_selection: "Clear Selection" + select_from_list: "Select from list" + more: "More" + statistics: "Statistics" + average: "Average" + min: "Min" + max: "Max" + median: "Median" + slices: "Slices" + help: "Help" + or: "Or" + show_advanced_options: "Show advanced options" + insert_sample_text: "Insert sample text" + class: "Class" + filter: "Filter" + ontology: "Ontology" + type: "Type" + context: "Context" + umls_sem_type: "UMLS Sem Type" + matched_ontology: "matched ontology" + matched_class: "Matched class" + score: "Score" + negation: "negation" + experience: "Experience" + temporality: "Temporality" + certainty: "Certainty" + format_results: "Format results as " + reproduce_results: "Reproduce these results using the " + additional_parameters: "Additional Parameters Explained at " + input: "Input" + text: "Text" + output: "Output" + ontology_sets: "Ontology sets" + insert_sample_input: "Insert sample input" + weights_configuration: "Weights Configuration" + coverage: "Coverage" + accept: "Accept" + knowledge_detail: "Knowledge Detail" + specialization: "Specialization" + max_ontologies_per_set: "Maximum number of ontologies per set" + paste_input_text: "Paste a paragraph of text or keywords to use in calculating ontology recommendations" + get_recommendations: "Get recommendations" + select_ontologies_list: "Select ontologies"