AgroPortal 1.4 (beta) released - Harnessing the power of metadata
Clement Jonquet
Title: Harnessing the power of metadata to visualize the landscape of agronomical ontologies
Tag: https://github.com/sifrproject/bioportal_web_ui/releases/tag/vAgro1.4
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.
Contact us at agroporta...@lirmm.fr
AgroPortal release notes: https://github.com/agroportal/documentation/wiki/Release-notes
Best regards
The AgroPortal team ;)
Dr. Clement JONQUET - PhD in Informatics - Assistant Professor
University of Montpellier
Coordinator of the SIFR and AgroPortal projects
Visiting scholar, Stanford University (EU Marie Curie fellow)
@Montpellier : +33/4 67 14 97 43
@Stanford : +1 650 723 6725