[Esip-agclimate] Fw: [EXTERNAL] [rda-agrdatainterop-ig][rda-fairsharing-wg][vocabulary_services][rda-agrisemantics-wg][rda-france] Fwd: [agroportal-support] AgroPortal 2.0 released – synchronization with OntoPortal, tons of new content and much more

Wed Oct 28 13:04:27 EDT 2020

fyi

________________________________
From: rda-agrdatainterop-ig at rda-groups.org <rda-agrdatainterop-ig at rda-groups.org> on behalf of jonquet via Agricultural Data Interest Group (IGAD) <rda-agrdatainterop-ig at rda-groups.org>
Sent: Wednesday, October 28, 2020 11:59 AM
To: subirats via Agricultural Data Interest Group (IGAD) <rda-agrdatainterop-ig at rda-groups.org>; Sophie Aubin <rda-agrisemantics-wg at rda-groups.org>; DAVECARR via FAIRsharing Registry WG: connecting data and metadata standards, repositories and policies <rda-fairsharing-wg at rda-groups.org>; Francoise Genova via RDA in France <rda-france at rda-groups.org>; ylefranc via Vocabulary Services IG <vocabulary_services at rda-groups.org>
Subject: [EXTERNAL] [rda-agrdatainterop-ig][rda-fairsharing-wg][vocabulary_services][rda-agrisemantics-wg][rda-france] Fwd: [agroportal-support] AgroPortal 2.0 released – synchronization with OntoPortal, tons of new content and much more

FYI for relavant/interested RDA groups.

Bye
Clement

Début du message réexpédié :

De: Clement Jonquet <jonquet at lirmm.fr<mailto:jonquet at lirmm.fr>>
Objet: [agroportal-support] AgroPortal 2.0 rel eased – synchronization with OntoPortal, tons of new content and much more
Date: 28 octobre 2020 à 16:37:24 UTC+1
À: agroportal-users at lirmm.fr<mailto:agroportal-users at lirmm.fr>, d2kab-public at lirmm.fr<mailto:d2kab-public at lirmm.fr>
Cc: agroportal-support at lirmm.fr<mailto:agroportal-support at lirmm.fr>, support at bioontology.org<mailto:support at bioontology.org>
Répondre à: Clement Jonquet <jonquet at lirmm.fr<mailto:jonquet at lirm
%20m.fr>>

Dear all,

We are pleased to announce the 2.0 release of the AgroPortal vocabulary and ontology repository:
http://agroportal.lirmm.fr/<https://urldefense.proofpoint.com/v2/url?u=http-3A__agroportal.lirmm.fr_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=qd45GsP229TUYf6UL0Vw5geuzs2MMW1RgI2vWC5KRg8&e=>

>From a technical perspective:

  *
AgroPortal is now based on OntoPortal 3.0<https://urldefense.proofpoint.com/v2/url?u=https-3A__ontoportal.org_ontoportal-2Dvirtual-2Dappliance-2Drelease-2D3-2D0-2Dis-2Dhere_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=r4JIC9IggTf8Y_EUwkxLoVpR_chtVl_UDvCLVfFUxtk&e=>. 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ontoportal-2Dlirmm&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=s4qFyTSVLyJgIu4Sq1Mz466Chdv27eQIvO6Gp3yB8Ow&e=>
Side projects, community feedback, issues is still on AgroPortal’s GitHub: https://github.com/agroportal<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_agroportal&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=67Ou7-QAvy_pMdi3nwY2VtzX70uWGe5OEw4BIPx_hn4&e=>
  *
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://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FRelease-5FNotes&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=xdojP-_T7J79ZreHtsoh8yFhVe_6ewJXvDm7Q6dsxsA&e=>. We congrat and acknowledge our collaborators at Stanford BMIR for all this work!
  *
AgroPortal Annotator now includes the latest version of the FastContext<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jianlins_FastContext&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=IINZre3Crjz6baRo_Ybp24kTJNFcoCZrVyjRTmzZTkM&e=> 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 40 0,000 mappings between concepts based on term reuse, term overlap and declared mappings in AgroPortal ontologies (EKAW 2020 paper<https://urldefense.proofpoint.com/v2/url?u=https-3A__hal.archives-2Douvertes.fr_lirmm-2D02945172_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=YKxZWferKyETYQ4hiTa-zRQt2lQfcs18RNCW_Kym4fU&e=>). 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://urldefense.proofpoint.com/v2/url?u=https-3A__hal.archives-2Douvertes.fr_lirmm-2D02945170_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=clvqqE4FoG2t7idUkLSHKfpMtgpGduCv6OPdXE1wKKk&e=>).
  *
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!

[https://lh3.googleusercontent.com/-e0rFmO-_7aPSZ7aCUQj1WBDiFcPpkMWT6G4uIGHazkX1VNDnDwJozTBMtlPN1m6wMBLjwv39w9fIMGg_VnieI-rc24skqpiPtkXZ5f33cI46mwEClZybWuLt-2J_yP1hyBB62Mj]

Feel free to contact us for information, feedback or to upload/access agronomy related semantic resources.
Documentation: https://github.com/agroportal/documentation/wiki<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_agroportal_documentation_wiki&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=37r7tqS6_xOL823SS_SBvNUw9784FgPcJh2nCdLZJJI&e=>
Support at: agroportal-support at lirmm.fr<mailto:agroportal-support at lirmm.fr>
Report issues to: https://github.com/agroportal/documentation/issues<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_agroportal_documentation_issues&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=MjxV1_7aUwb1qas8DKmOnEc5Ys_ZcEN9QrmCmDgateo&e=>

Acknowledgments:
AgroPortal is currently being developed within French ANR D2KAB project<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.d2kab.org_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=Oftvuq1OMASNHGrzrZNIXpbQ-RLNOteA4_xuHw1Dfk4&e=> (ANR-18-CE23-0017<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.agence-2Dnationale-2Drecherche.fr_Projet-2DANR-2D18-2DCE23-2D0017&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=-KJbRAv5SG_oWpW49nSdeO4vx_ioXu4IP0FwZhobOyU&e=>). It also receives or received support from ANR SIFR project<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.lirmm.fr_sifr&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=-z7TnJcJsAO1CYXjxtDhSruIZ9a4e0FhdaVmQjMSqvE&e=> (ANR-12-JS02-0010<https://urldefense.proofpoint.com/v2/url?u=https-3A__anr.fr_Projet-2DANR-2D12-2DJS02-2D0010&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=nnnqcwIz9XYOMH24a8hJIpW8wmvZMroBCEIx68u3Tv0&e=>), European Union H2020-MSCA SIFRm project<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.lirmm.fr_sifr&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=-z7TnJcJsAO1CYXjxtDhSruIZ9a4e0FhdaVmQjMSqvE&e=> (No 701771<https://urldefense.proofpoint.com/v2/url?u=https-3A__cordis.europa.eu_project_id_701771&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=2Uq-SHq_K8aPY8Q-4QJT4_wt2b_0QzPVaE1OIjgBiKk&e=>), the NUMEV Labex<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.lirmm.fr_numev_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=2EtmxxjJWCCw-UK5MYNmVOekgzVezRsY8L0edq6jqJA&e=> (ANR-10-LABX-0020<https://urldefense.proofpoint.com/v2/url?u=https-3A__anr.fr_ProjetIA-2D10-2DLABX-2D0020&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=i1cOti8jBDOcOrTKTQT5P_Ea5mSzRL-OTleIHt2pocc&e=>), the IBC of Montpellier project<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ibc-2Dmontpellier.fr_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=ZtBD4SrpwGd8M4jeOvCFqX0Zm5KS8DG1uENIj0OlhwM&e=> (ANR-11-BINF0002<https://urldefense.proofpoint.com/v2/url?u=https-3A__anr.fr_ProjetIA-2D11-2DBINF-2D0002&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=zJ6Q0dBAVCCuBrbDT0l3q0X-t8kbdbY1Omtw_DRQ6Ec&e=>), the Agro Labex<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.agropolis-2Dfondation.fr_The-2DLabEx-2DAGRO-3Flang-3Den&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=MMPhnHx6kvshTd5iyP8TF62zPWEluxlAlxaPB5Y_jKw&e=> (ANR-10-LABX-0001<https://urldefense.proofpoint.com/v2/url?u=https-3A__anr.fr_ProjetIA-2D10-2DLABX-2D0001&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=8kgma3n1ze5Kwsd0NkX0ya9b0gsiRQBiX8ApWn3LHhA&e=>) 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.lirmm.fr_sifr&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=-z7TnJcJsAO1CYXjxtDhSruIZ9a4e0FhdaVmQjMSqvE&e=>,  AgroPortal<https://urldefense.proofpoint.com/v2/url?u=http-3A__agroportal.lirmm.fr_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=qd45GsP229TUYf6UL0Vw5geuzs2MMW1RgI2vWC5KRg8&e=> and D2KAB<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.d2kab.org_&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=Oftvuq1OMASNHGrzrZNIXpbQ-RLNOteA4_xuHw1Dfk4&e=> 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.lirmm.fr_-7Ejonquet&d=DwMBaQ&c=ApwzowJNAKKw3xye91w7BE1XMRKi2LN9kiMk5Csz9Zk&r=img-rO8ZBhblrx41WBkIFetQkzEsdhT-s4UDDrJe0Xk&m=IdVCUkSavQJbeO9uqUs7NSP7cQNHJwleZ46v82TjylE&s=IkkgsjzQL8UsmzrX0EjL6FK_dDCE6q3zcZK3PTM-U-k&e=>

@MISTEA (L,M,M,J): +33/0 4 99 61 22 77
@LIRMM (V): +33/0 4 67 14 97 43
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