Pantheon Components Inventory
Applications and Data Source
Data Source and Use Cases
Applications and Use Cases

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Pantheon Components Inventory

The core of the GCP Platform are applications used by the end-users. The applications get data from various resources through the so-called data sources. What kind of data and how they can be searched for, it is defined by use cases, implemented by individual data sources.

This page shows graphically how many of these components exist and how they are connected. The graph nodes are linked to more detailed information, either by clicking on them, or by a small help tooltip, shown when your mouse hover over the node. Some application nodes even allow to start the application.

Colors: The blue thinner lines linking Use Case nodes represent inheritance (the empty arrow points to the parent use case). Other colors may be customized - so they may divert from what is said here: the orange nodes are not used (or, for the Use Cases nodes, they are not use directly). Empty black ellipses with data sources represent not-yet existing or not yet deployed data sources.

If you are a developer and you wish to update this page, either to add your new component, or to update version of the existing one, read these short instructions how to do it.

Please report problems and suggestions to Martin Senger

[this page was generated: Thu Sep 10 14:35:59 SGT 2009]

GenDiversity

Web Application allowing to recover, manipulate, combine and export genotyping data from various data sources.

Authority CIRAD
Version  
Contact Gautier Sarah,Manuel Ruiz,Aminah Keliet
Public URL Start/View application
URL for developers  
Which crop barley, chickpea, coconut, lentil, musa, rice, sorghum, wheat
Usage  
Germplasm Browser (Zeus)

The Germplasm Browser applies the GCP standards to the International Crop Information System (ICIS) database schemata to serve germplasm, study, passport, trait, and marker data through GCP data sources that query against germplasm pedigrees and germplasm lists in the ICIS Genealogy Management System (GMS) and study data in the ICIS Data Management System (DMS)

The ICIS is a database system that provides integrated management of global information on genetic resources and crop cultivars.

Authority CRIL
Version 1.5
Contact Martin Senger,Mylah Anacleto,Manfred Cardenas,Alexander Caneda
Public URL IRIS Maintained at IRRI
IWIS maintained at CIMMYT
IMIS maintained at CIMMYT
URL for developers IRIS maintained at IRRI
IWIS hosted in IRRI
IMIS hosted in IRRI
Which crop rice, wheat, maize
Usage View ICIS Web Project Documentation
Cropfinder (Zeus)

The website for cross-study queries.

Authority IRRI
Version  
Contact Martin Senger,Mylah Anacleto,Manfred Cardenas,Alexander Caneda
Public URL  
URL for developers IWIS Cross study browser hosted in IRRI
IRIS Cross study browser maintained at IRRI
IWIS Cross study browser maintained at CIMMYT
Which crop wheat, rice, maize
Usage View the ICIS Cropfinder Project Documentation
Passport Website-IRRI Passport(Zeus)

A Website for Querying IRRI Passport Data.

Authority IRRI
Version  
Contact Martin Senger,Mylah Anacleto,Manfred Cardenas
Public URL  
URL for developers IRIS Passport query hosted in IRRI
Which crop any
Usage View Passport Web Project Documentation
Passport Website-Bioversity International Passport(Zeus)

A Website for Passport Query across BioMOBY Services to the Central Registry.

Authority IRRI
Version  
Contact Martin Senger,Mylah Anacleto,Manfred Cardenas
Public URL  
URL for developers View application
Which crop any
Usage View Passport Web Project Documentation
GetAccessionsByFeatures 1.0.2

This use case requests the accession IDs that match the search simple features...

GetFeaturesByAccessionId 1.0.1

The input to this use case is a SimpleIdentifier object that has a mandatory ID field ("uniqueIdentifier") filled...

RetrieveControlledVocabulary 1.1.0

This use case extends the "RetrieveOntology" use case...

RetrieveDetectedVariants 1.2.5

This use case returns list of DetectedVariant entities...

RetrieveDocumentedFeatureTypes 1.0.0

A simple query by name on a Feature "type" attribute can be productively used to identify the list of ontology terms with associated meta-data...

RetrieveFactorLevels 1.0.0

This use case returns list of Constraint entities...

RetrieveFactorsAcrossStudies 1.0.1

Retrieve factors containing distinct combinations of property, scale and method from one or more studies

RetrieveFeatureDescriptors 2.0.0

A central model in the core GCP domain model is the Feature class...

RetrieveFeatureOntology 1.0.0

A central model in the core GCP domain model is the Feature class...

RetrieveGenomicFeatureDetectors 1.1.0

This use case returns list of GenomicFeatureDetector entities...

RetrieveGenotypeDataset 1.0.1

The user will select one or more germplasm (samples), studies, markers, alleles...

RetrieveGenotypeStudies 1.2.3

This use case returns list of GenotypeStudy entities...

RetrieveGenotypedGermplasms 1.1.0

This use case returns list of Germplasm that has been genotyped...

RetrieveGermplasmByPhenotypicCharacteristics 1.2.5

The main purpose is to find all germplasm records that have the given phenotype, or combination of phenotypes, indexed and queried by various levels of description: plant anatomy or developmental ontology, trait ontology of full phenotypes (trait and trait value assignments)...

RetrieveGermplasmIdentifierByPhenotype 1.0.2

The main purpose is to find all germplasm records that have the given phenotype, or combination of phenotypes...

RetrieveGermplasmSets 1.0.2

This use case refers to the retrieval of sets of Germplasm where such sets are formally managed for example, within the list management table of the International Crop Information System (ICIS)...

RetrieveGermplasmStudies 1.2.8

This use case returns list of GermplasmStudy entities...

RetrieveGermplasms 1.6.0

These use cases refer to the querying of germplasm data...

RetrieveOntology 1.0.0

An ontology is a controlled vocabulary ("dictionary") of defined concepts Each concept instance in an ontology is a "term"...

RetrieveOntologyData 1.0.3

An ontology is a controlled vocabulary ("dictionary") of defined concepts Each concept intance in an ontology is a "term"...

RetrieveOntologyTerms 1.1.0

This use case (now) extends the "RetrieveOntology" use case...

RetrievePassportTableReference 1.0.1

This use case returns TableReference object consisting of a url which points to a csv file that contains passport data...

RetrieveReference 1.0.1

This use case provides a base use case for all Reference use cases by providing details of the returned attributes, but not searchable attributes...

RetrieveSimpleControlledVocabulary 1.1.0

This use case is a highly simplified version of the "RetrieveControlledVocabulary" use case...

RetrieveSimpleFeatureDescriptors 1.0.0

A central model in the core GCP domain model is the Feature class...

RetrieveStudies 1.4.2

This use case returns a basic list of Study entities with limited annotation...

RetrieveStudyEffects 1.2.7

This use case returns list of Effect entities...

RetrieveStudyFactors 1.0.0

Retrieve factors containing distinct combinations of property, scale and method from one or more studies...

RetrieveStudyFeatureConstraints 1.0.2

This use case returns list of Constraint entities that is related to a specific study feature...

RetrieveStudyFeatures 1.0.0

Retrieve study features from one or more studies...

RetrieveStudyFeaturesAcrossStudies 1.0.1

Retrieve study features from one or more studies...

RetrieveStudyObservationUnits 1.2.6

This use case returns list of ValueSet entities...

RetrieveStudyTableReference 1.0.0

This use case returns a single TableReference object...

RetrieveStudyTabularData 1.0.0

This use case returns a single TabularData object...

RetrieveStudyVariates 1.0.0

Retrieve variates containing distinct combinations of property, scale and method from one or more studies

RetrieveTableReference 1.0.1

This use case provides a base use case for all Table Reference use cases by providing details of the returned attributes, but not searchable attributes...

RetrieveTableReferenceWithGenericConstraints 1.0.1

Extends the Retrieve Table Reference use case by providing a generic way to constrain the row and columns by column id or name, and/or row id or name of a file...

RetrieveTabularData 1.0.0

The GCP domain model documents a TabularData object to be of the following Java interface structure: public interface TabularData extends Value ...

RetrieveTabularDataAcrossStudies 1.0.4

This use case returns a single TabularData object...

RetrieveTabularDataValueAt 1.2.5

This use case returns list of Value entities...

RetrieveTabularDataWithGenericConstraints 1.0.0

Extends the Retrieve Tabular Data use case by providing a genetic way to constrain the row and columns by column id or name, and/or row id or name The searchable attributes on this use case are somewhat very generic...

RetrieveVariateDataRange 1.2.4

This use case returns list of Constraint entities...

RetrieveVariatesAcrossStudies 1.0.2

Retrieve variates containing distinct combinations of property, scale and method from one or more studies

IRIS_LOCAL_DS
Id http://irislocal.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Tabular Data
Reference
Germplasm Study
GenomicFeatureDetector
Detected Variant
Germplasm
Study Effects
GermplasmSet
Feature Type as Ontology Term
Study
Simple Feature
Study Observation Units
Variate Data Range
Factor Levels
TableReference
Genotype Study
IWIS_LOCAL_DS
Id http://iwislocal.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Tabular Data
Reference
Germplasm Study
GenomicFeatureDetector
Detected Variant
Germplasm
Study Effects
GermplasmSet
Feature Type as Ontology Term
Study
Simple Feature
Study Observation Units
Variate Data Range
Factor Levels
TableReference
Genotype Study
IMIS_LOCAL_DS
Id http://imislocal.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Tabular Data
Reference
Germplasm Study
GenomicFeatureDetector
Detected Variant
Germplasm
Study Effects
GermplasmSet
Feature Type as Ontology Term
Study
Simple Feature
Study Observation Units
Variate Data Range
Factor Levels
TableReference
Genotype Study
IWIS-CF-DS
Id http://iwiscf.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Tabular Data
Reference
Variate
Germplasm Study
Tabular Data
GenomicFeatureDetector
Table Reference
Detected Variant
Study Features
Germplasm
Study Effects
GermplasmSet
Feature Type as Ontology Term
Study
Simple Feature
Factor
Study Observation Units
Variate Data Range
Factor Levels
TableReference
Genotype Study
IRIS-CF-DS
Id http://iriscf.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Tabular Data
Reference
Variate
Germplasm Study
Tabular Data
GenomicFeatureDetector
Table Reference
Detected Variant
Study Features
Germplasm
Study Effects
GermplasmSet
Feature Type as Ontology Term
Study
Simple Feature
Factor
Study Observation Units
Variate Data Range
Factor Levels
TableReference
Genotype Study
IMIS-CF-DS
Id http://imiscf.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Tabular Data
Reference
Variate
Germplasm Study
Tabular Data
GenomicFeatureDetector
Table Reference
Detected Variant
Study Features
Germplasm
Study Effects
GermplasmSet
Feature Type as Ontology Term
Study
Simple Feature
Factor
Study Observation Units
Variate Data Range
Factor Levels
TableReference
Genotype Study
Bioversity Passport Descriptors
Id webmoby.bioversityInternational.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Accession Unique Identifier
Ontology Term
Simple Feature
Ontology
PASSPORT_IRIS_LOCAL_DS
Id http://passport.irislocal.irri.org
How to use it Descriptor page
Validation Not yet included here
Provided data types Reference
Accession Unique Identifier
Ontology Term
Simple Feature
Ontology
TableReference