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Fwd: [agroportal-support] AgroPortal 2.0 released – synchronization with OntoPortal, tons of new content and much more

From: Clement Jonquet <jonquet@lirmm.fr>
Date: Thu, 29 Oct 2020 18:53:15 +0100
Message-Id: <01B95D30-1A4E-4BDF-AE83-C974DB4CC014@lirmm.fr>
In between 2 lockdown in France, we made it happen ;)

> Dear all, 
> We are pleased to announce the 2.0 release of the AgroPortal vocabulary and ontology repository:
> http://agroportal.lirmm.fr/ <http://agroportal.lirmm.fr/>
> From a technical perspective:
> AgroPortal is now based on OntoPortal 3.0 <https://ontoportal.org/ontoportal-virtual-appliance-release-3-0-is-here/>. 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 <https://github.com/ontoportal-lirmm> 
> Side projects, community feedback, issues is still on AgroPortal’s GitHub: https://github.com/agroportal <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 <https://www.bioontology.org/wiki/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 <https://github.com/jianlins/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 <https://hal.archives-ouvertes.fr/lirmm-02945172/>). 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 <https://hal.archives-ouvertes.fr/lirmm-02945170/>).  
> 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 <https://github.com/agroportal/documentation/wiki> 
> Support at: agroportal-support@lirmm.fr <mailto:agroportal-support@lirmm.fr> 
> Report issues to: https://github.com/agroportal/documentation/issues <https://github.com/agroportal/documentation/issues> 
> Acknowledgments: 
> AgroPortal is currently being developed within French ANR D2KAB project <http://www.d2kab.org/> (ANR-18-CE23-0017 <http://www.agence-nationale-recherche.fr/Projet-ANR-18-CE23-0017>). It also receives or received support from ANR SIFR project <http://www.lirmm.fr/sifr> (ANR-12-JS02-0010 <https://anr.fr/Projet-ANR-12-JS02-0010>), European Union H2020-MSCA SIFRm project <http://www.lirmm.fr/sifr> (No 701771 <https://cordis.europa.eu/project/id/701771>), the NUMEV Labex <https://www.lirmm.fr/numev/> (ANR-10-LABX-0020 <https://anr.fr/ProjetIA-10-LABX-0020>), the IBC of Montpellier project <http://www.ibc-montpellier.fr/> (ANR-11-BINF0002 <https://anr.fr/ProjetIA-11-BINF-0002>), the Agro Labex <https://www.agropolis-fondation.fr/The-LabEx-AGRO?lang=en> (ANR-10-LABX-0001 <https://anr.fr/ProjetIA-10-LABX-0001>) as well as from University of Montpellier, CNRS and INRAE.
> -------------------------------------------------------------------------------------------
> Dr. Clement JONQUET  –  PhD in Informatics
> Associate Research Scientist – INRAE (MISTEA)
> Associate Professor – University of Montpellier (LIRMM)
> Coordinator of the SIFR <http://www.lirmm.fr/sifr>,  AgroPortal <http://agroportal.lirmm.fr/> and D2KAB <http://www.d2kab.org/> projects
> jonquet@lirmm.fr <mailto:jonquet@lirmm.fr> or clement.jonquet@inrae.fr <mailto:clement.jonquet@inrae.fr> 
> http://www.lirmm.fr/~jonquet <http://www.lirmm.fr/~jonquet>
> @MISTEA (L,M,M,J): +33/0 4 99 61 22 77
> @LIRMM (V): +33/0 4 67 14 97 43
> -------------------------------------------------------------------------------------------

Received on Thursday, 29 October 2020 17:53:36 UTC

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