MOD: Métadonnées pour l'ontologie Description et publication
MOD: Metadata for Ontology Description and publication
An entity responsible for making contributions to the resource.
An entity primarily responsible for making the resource.
DCT: a related resource that is substantially the same as the pre-existing described resource, but in another format.
The level of formality of an ontology.
Information about a knowledge representation paradigm a particular language adheres to.
Information about the ontology engineering methodology.
A tool used to create the ontology.
Information about the language in which the ontology is implemented.
This class subsumes types of ontologies according to well-known classifications in the
Ontology Engineering literature.
A rate at which something recurs.
A method by which resources are added to a collection.
A plan or course of action by an authority, intended to influence and determine decisions, actions, and other matters.
A statement about the intellectual property rights (IPR) held in or over a Resource, a legal document giving official permission to do something with a resource, or a statement about access rights.
The evaluation criterias, essentially the various aspects that are used in validating the quality of an ontology. These aspects may include for example, accuracy, adaptability, accessibility, clarity, completeness, computational efficiency, conciseness, informativeness, uniqueness, relevancy, reliability, usefulness and organizational fitness.
A methodology that is being followed in evaluating an ontology, e.g., application based approach, assessment by human, data driven approach and golden standard.
1
1
1
1
1
1
1
1
1
1
The results of evaluating an ontology. An ontology can have more than one evaluations.
An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
An agent (eg. person, group, software or physical artifact).
An image.
An organization.
A person.
A project (a collective endeavour of some kind).
AGROOE
Alpha
AGROOE is an ontology used to test the metadata extraction, AGROOE is an ontology to illustrate how to describe their ontologies.
Ontology
http://stageportal.lirmm.fr/ontologies/is%20primary%20topic%20of
http://lirmm.fr/2015/resource/AGROOE_c_01
http://omv.ontoware.org/2005/05/ontology#Ontology
http://omv.ontoware.org/2005/05/ontology#OntologyDomain
http://omv.ontoware.org/2005/05/ontology#OntologyEngineeringMethodology
http://omv.ontoware.org/2005/05/ontology#OntologyEngineeringTool
http://omv.ontoware.org/2005/05/ontology#OntologyTask
http://omv.ontoware.org/2005/05/ontology#OntologyType
http://omv.ontoware.org/2005/05/ontology#Organisation
http://omv.ontoware.org/2005/05/ontology#Person
http://purl.org/dc/terms/Agent
http://xmlns.com/foaf/0.1/Person
Alpha 2.0
http://agroportal.lirmm.fr/
http://agroportal.lirmm.fr
http://agroportal.lirmm.fr/
Agronomic Linked Data
AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. The aim of the Agronomic Linked Data (AgroLD) project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.
pierre.larmande@ird.fr
Agronomic Linked Data Project
ANAEETHES
biotic environment
ecosystem
spatio-temporal characteristics
http://data.agroportal.lirmm.fr/ontologies/ANAEETHES/download
Alpha
The AnaEE thesaurus aims to provide a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. It has been developed within the framework of the AnaEE-France infrastructure through an iterative process combining both top down and bottom up approaches: import of concepts from other thesauri and collection of concepts used in the AnaEE data bases and/or modeling platforms.
http://lexvo.org/id/iso639-3/eng
http://lexvo.org/id/iso639-3/fra
Agricultural Research
Earth and Environment
Natural Resources
Technology and Engineering
2017-03-22T00:00:00+00:00
2017-03-22T00:00:00
http://opendata.inra.fr/anaeeThes/c2_942
anaee_thesaurus@inra.fr
http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Unit
http://opendata.inra.fr/anaeeThes/c2_112
http://opendata.inra.fr/anaeeThes/c2_115
http://opendata.inra.fr/anaeeThes/c2_2445
http://opendata.inra.fr/anaeeThes/c2_2934
http://opendata.inra.fr/anaeeThes/c2_2941
http://opendata.inra.fr/anaeeThes/c2_3022
http://opendata.inra.fr/anaeeThes/c_1401956207670
http://opendata.inra.fr/anaeeThes/c_1402038921919
http://opendata.inra.fr/anaeeThes/c_1403018120212
http://opendata.inra.fr/anaeeThes/c_9178f420
http://opendata.inra.fr/anaeeThes/c_b177c123
false
http://data.agroportal.lirmm.fr/ontologies/ANAEETHES/submissions/1
1.0
http://sparql.agroportal.lirmm.fr/test
http://dx.doi.org/10.15454/1.4894016754286177E12
http://dx.doi.org/10.15454/1.4894016754286177E12
AnaEE France
The AnaEE semantics group aims to provide a semantics vocabularies (thesaurus and ontology for the description of the study of continental ecosystems and their biodiversity.
anaee_thesaurus@inra.fr
https://www.anaee-france.fr/fr/
ANAEE Semantics
Anaee Semantics Project
Bioversity International
www.cgiar.org
CGIAR
Cathy H. Wu
Cecilia Arighi
jonquet@lirmm.fr
Modeling, processing and analysis of large scale data in biology, health, agronomy and environment.
pierre.larmande@ird.fr
Computational Biology Institute Project
https://creativecommons.org/licenses/by/3.0/
Crop Ontology Curation Tool
Crop Ontology Helpdesk
Crop Ontology is a service of the Integrated Breeding Platform, and targets agricultural data annotation. The project is led by Bioversity International in collaboration with the CGIAR and other partners. Crop Ontology centralizes concepts defined by breeders to annotate their data egarding germplasm, phenotypes, trial location, environment and design, plant anatomy, and plant development.
e.arnaud@cgiar.org
http://www.cropontology.org/
The Crop Ontology project
Darren A. Natale
Darren Natale
http://purl.obolibrary.org/obo/doid.owl
lschriml@som.umaryland.edu
lynn.schriml@gmail.com
http://disease-ontology.org
https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/master/doc
Disease ontology
e.arnaud@cgiar.org
Elizabeth Arnaud
Esther Dzalé-Yeumo
Food & Agriculture Organization
http://purl.obolibrary.org/obo/go.owl
GO
Biology
biological process
cellular component
molecular function
gene function
The use of GO terms by collaborating databases facilitates uniform queries across all of them. Controlled vocabularies are structured so they can be queried at different levels; for example, users may query GO to find all gene products in the mouse genome that are involved in signal transduction, or zoom in on all receptor tyrosine kinases that have been annotated. This structure also allows annotators to assign properties to genes or gene products at different levels, depending on the depth of knowledge about that entity.
48549
0
9
http://data.agroportal.lirmm.fr/ontologies/GO/download
Production
The GO defines concepts/classes used to describe gene function, and relationships between these concepts. It classifies functions along three aspects: molecular function (molecular activities of gene products), cellular component (where gene products are active), biological process (pathways and larger processes made up of the activities of multiple gene products).
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases. Founded in 1998, the project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database (SGD) and the Mouse Genome Database (MGD). The GO Consortium (GOC) has since grown to incorporate many databases, including several of the world's major repositories for plant, animal, and microbial genomes. The GO Contributors page lists all member organizations.
http://lexvo.org/id/iso639-3/eng
http://purl.org/dc/elements/1.1/
2017-04-06T18:08:56+02:00
2017-03-28T00:00:00
2017-03-30T00:00:00
2017-03-31T00:00:00
2017-04-01T00:00:00
2017-04-06T00:00:00
http://purl.obolibrary.org/obo/go.obo
http://purl.obolibrary.org/obo/GO_0015219
gene_ontology
https://github.com/geneontology/go-ontology/issues/
go@geneontology.org
http://geneontology.org/page/go-mailing-lists
https://sourceforge.net/projects/geneontology/
http://purl.obolibrary.org/obo/GO_0003674
http://purl.obolibrary.org/obo/GO_0005575
http://purl.obolibrary.org/obo/GO_0008150
false
http://data.agroportal.lirmm.fr/ontologies/GO/submissions/72
http://purl.obolibrary.org/obo/go/releases/2017-03-08/go.owl
2017-03-08
http://sparql.agroportal.lirmm.fr/test
http://geneontology.org/sites/default/files/u425/diag-ontology-graph.gif
http://www.geneontology.org/
http://geneontology.org/sites/default/files/go-logo-icon.png
http://geneontology.org/page/ontology-documentation
http://geneontology.org/page/publications
cvs version: $Revision: 38972 $, Includes Ontology(OntologyID(OntologyIRI())) [Axioms: 18 Logical Axioms: 0]
Gene ontology
http://www.geneontology.org/
Gene Ontology Consortium
http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
Gene Ontology plus
CO_715
Corrugation
Crop research ontology
Sub-irrigation
Wild flooding
crop study
environmental conditions
experimental design
The concepts of the CO are used to curate agronomic databases and describe the data.
256
0
2
Production
Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation.
http://lexvo.org/id/iso639-3/eng
2017-03-09T18:03:17+01:00
2017-03-09T18:03:17+01:00
co
helpdesk@cropontology-curationtool.org
r.shrestha2@cgiar.org
http://purl.obolibrary.org/obo/CO_715_0000000
http://purl.obolibrary.org/obo/CO_715_0000207
http://purl.obolibrary.org/obo/CO_715_0000208
http://purl.obolibrary.org/obo/CO_715_0000209
http://purl.obolibrary.org/obo/CO_715_0000210
http://purl.obolibrary.org/obo/CO_715_0000211
http://purl.obolibrary.org/obo/CO_715_0000212
http://purl.obolibrary.org/obo/CO_715_0000213
http://purl.obolibrary.org/obo/CO_715_0000214
2012
http://www.cropontology.org/
http://www.cropontology.org/
IBP Crop Research Ontology
https://www.integratedbreeding.net/
Integrated Breeding Platform
Leslie Arminski
Lynn Schriml
https://github.com/sifrproject/MOD-Ontology/blob/master/mod-v1.2.owl
MOD
To describe the vocabularies, e.g., ontology, classification, metadata, etc.
Agent
Group
Ontology
Ontology type
Project
Ontology metadata
644
24
https://github.com/sifrproject/MOD-Ontology/blob/master/mod-v1.2.owl
MOD 1.2 is ready for production use.
A metadata vocabulary to describe and publish ontologies on the Web.
http://www.isibang.ac.in/ns/mod
https://github.com/sifrproject/MOD-Ontology
http://lexvo.org/id/iso639-3/eng
MOD 1.0 and AgroPortal
Ontology metadata
Metadata for Ontology Description and Publication
2016-09-15T00:00:00
2017-01-10T00:00:00
mod
http://www.isibang.ac.in/ns/mod#
https://github.com/sifrproject/MOD-Ontology/issues
(1) List out the totals number ontologies in the triple store?
(2) Which ontology editor is used most in constructing the ontologies?
(3) How many classes and properties an ontology has?
53
35
http://www.isibang.ac.in/ns/mod#Activity
http://www.isibang.ac.in/ns/mod#Agent
http://www.isibang.ac.in/ns/mod#Frequency
http://www.isibang.ac.in/ns/mod#Group
http://www.isibang.ac.in/ns/mod#MethodOfAccrual
http://www.isibang.ac.in/ns/mod#Ontology
http://www.isibang.ac.in/ns/mod#Policy
http://www.isibang.ac.in/ns/mod#Project
http://www.isibang.ac.in/ns/mod#RightsStatement
http://omv.ontoware.org/2005/05/ontology#
http://purl.org/dc/elements/1.1/
http://purl.org/dc/terms/
http://purl.org/pav/
http://usefulinc.com/ns/doap/
http://www.w3.org/2004/02/skos/core#
http://www.w3.org/ns/prov#
http://xmlns.com/foaf/0.1
Metadata for Ontology Description and Publication Ontology
This project consists in building an OWL ontology to capture metadata information for ontologies.
This is somehow a follow-up of http://omv2.sourceforge.net
A MOD Ontology 1.0 was published by @biswanathdutta in September 2015: http://dcpapers.dublincore.org/pubs/article/view/3758
We are currently working on MOD 1.2 which will partially include properties listed by @jonquet and @antooland implemented within AgroPortal (https://github.com/agroportal): https://github.com/agroportal/documentation/tree/master/metadata
Contacts: Biswanath Dutta bisu@drtc.isibang.ac.in (@biswanathdutta) Clement Jonquet jonquet@lirmm.fr (@jonquet)
false
www.isibang.ac.in/~bisu/ontology/mod-ontology-09092016.owl
http://www.isibang.ac.in/ns/mod/1.2
MOD version 1.2. The preceeding version is MOD1.1.
http://www.isibang.ac.in/ns/mod.html
Metadata for Ontology Description and publication
NCBITAXON
Viroids
Viruses
cellular organisms
plasmids
906907
0
3
https://www.ncbi.nlm.nih.gov/home/download.shtml
Production
The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.
https://bioportal.bioontology.org/ontologies/NCBITAXON
http://lexvo.org/id/iso639-3/eng
Taxonomic Classifications of Organisms
2015-06-09T17:38:59-07:00
2015-06-23T00:00:00
http://purl.obolibrary.org/obo/ncbitaxon.owl
https://www.ncbi.nlm.nih.gov/taxonomy
http://purl.bioontology.org/ontology/NCBITAXON/201174
ncbitaxon
info@ncbi.nlm.nih.gov
http://purl.bioontology.org/ontology/NCBITAXON/10239
http://purl.bioontology.org/ontology/NCBITAXON/12884
http://purl.bioontology.org/ontology/NCBITAXON/131567
http://purl.bioontology.org/ontology/NCBITAXON/28384
2015AA
http://agroportal.lirmm.fr/ontologies/NCBITAXON
https://www.ncbi.nlm.nih.gov/
https://www.ncbi.nlm.nih.gov/portal/portal3rc.fcgi/4117326/img/28977
https://doi.org/10.1093/nar/gki062
https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/
NCBITAXON ontology
https://www.nsf.gov/
National Science Foundation
http://oboedit.org/
OBO-Edit
OBO Foundry
Oregon State University
http://proconsortium.org/pirwww/about/staff.shtml
PIR
http://proconsortium.org
PRO Consortium
http://www.planteome.org/
Planteome
Pankaj Jaiswal
Pierre Larmande
The Planteome Project is a centralized platform where reference ontologies for plants will be used to access plant genomics data.
jaiswalp@science.oregonstate.edu
Planteome Project
Protein Information Resource
http://purl.obolibrary.org/obo/pr.owl
PR
gene
organism
protein
protein coding gene
amino acids
genes
immunology
protein
proteomics
uniprot knowledgebase
83656
0
11
http://data.agroportal.lirmm.fr/ontologies/PR/download?download_format=rdf
Production
An ontological representation of protein-related entities. The PRotein Ontology (PRO) formally defines taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes.
The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to UniProtKB in that PRO's organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO's representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments.
http://lexvo.org/id/iso639-3/eng
2014-04-13T00:00:00+00:00
2015-06-30T00:00:00
http://purl.obolibrary.org/obo/pr.owl
http://purl.obolibrary.org/obo/PR_000018263
pr
http://purl.obolibrary.org/obo/
dan5@georgetown.edu
pirmail@georgetown.edu
https://sourceforge.net/projects/pro-obo/
http://purl.obolibrary.org/obo/BFO_0000019
http://purl.obolibrary.org/obo/BFO_0000040
http://purl.obolibrary.org/obo/SO_0000110
false
41.0
http://pir.georgetown.edu/pro/pro_sparql.shtml
http://proconsortium.org/pirwww/images/Pro2.png
http://proconsortium.org/pro/
https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.pn
http://proconsortium.org/pirwww/about/publication.shtml
http://proconsortium.org/pirwww/support/help.shtml
Protein Ontology
Research Data Allianca
The Wheat Data Interoperability Working Group aims to provide a common framework for describing, representing linking and publishing Wheat data with respect to open standards. The RDA WDI group has a specific slice in AgroPortal: http://wheat.agroPortal.lirmm.fr
edzale@versailles.inra.fr
r.fulss@cgiar.org
https://www.rd-alliance.org/groups/wheat-data-interoperability-wg.html
RDA Wheat Interoperability Working Group
http://www.obofoundry.org/ontology/ro
Relations Ontology
Richard Fulss
Rosemary Shrestha
Sequence Types and Features Ontology
TermGenie 1.0
Unified Medical Language System
http://purl.obolibrary.org/obo/uberon.owl
University of Montpellier
This VEST-AgroPortal provides a global map of existing vocabularies for the exchange of data in the field of food and agriculture. The directory is the result of the merging of records from two different sources: the VEST Registry (a registry of vocabularies of all types and all formats) and the AgroPortal (a repository of ontologies).
valeria.pesce@fao.org
http://vest.agrisemantics.org/
VEST-AgroPortal Map of Standards
Valeria Pesce
Ontology
Wheat Data Interoperability working group