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AgroPortal 1.4 (beta) released - Harnessing the power of metadata

From: Clement Jonquet <jonquet@lirmm.fr>
Date: Tue, 4 Jul 2017 11:25:05 +0200
To: <agroportal-support@lirmm.fr>
Cc: <agroportal-users@lirmm.fr>
Message-ID: <03d601d2f4a7$8054e9d0$80febd70$@lirmm.fr>
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>
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>
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>
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&display_links=false&disp
lay_context=false&apikey=1de0a270-29c5-4dda-b043-7c3580628cd5>
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>
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
<https://workshop.inra.fr/in-ovive-2017> IN-OVIVE 2017 workshop and
<http://www.efita2017.org/> EFITA 2017 conference's demonstration session
in Montpellier, week of July 3rd, 2017.

 

Contact us at  <mailto:agroportal-support@lirmm.fr>
agroportal-support@lirmm.fr 

 

AgroPortal release notes:
<https://github.com/agroportal/documentation/wiki/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  <http://www.lirmm.fr/sifr/> SIFR and
<http://agroportal.lirmm.fr/> AgroPortal projects

Visiting scholar, Stanford University (EU Marie Curie fellow)

 

 <mailto:jonquet@lirmm.fr> jonquet@lirmm.fr

 <http://www.lirmm.fr/~jonquet> http://www.lirmm.fr/~jonquet 

 

@Montpellier : +33/4 67 14 97 43

@Stanford       : +1 650 723 6725

 

 

 

 
Received on Tuesday, 4 July 2017 09:26:21 UTC

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