Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Clement Jonquet jonquet at lirmm.fr
Wed Oct 28 08:37:24 PDT 2020


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 at lirmm.fr <mailto:agroportal-support at 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 at lirmm.fr <mailto:jonquet at lirmm.fr> or clement.jonquet at inrae.fr <mailto:clement.jonquet at 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
-------------------------------------------------------------------------------------------

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20201028/876d28c4/attachment-0001.html>


More information about the bioontology-support mailing list