GCP Biomoby

List of BioMoby Web Services (By Institute)

IRRI

Name of Web Service Input Output
getAccessionByGermplasm Specified genetic resource accession (identifier) Accession that a given germplasm (identifier) belongs to (if applicable)
getAccessionPassport Specified genetic resource accession (identifier) Accession that a given germplasm (identifier) belongs to (if applicable)
getGermplasmByAccession Germplasm identifier corresponding to (the "FoundingGermplasm" of) an Accession List of all germplasm identifiers (belonging to the Management Neighbourhood) of the Accession
getGermplasmDetails germplasm identifier (List of) full details about specified germplasm
getGermplasmByName Search string of a germplasm name (List of) germplasm identifier(s) whose name(s) match
getStudies germplasm identifier List of identifiers of germplasm studies where samples of the given germplasm were used in the experiment
getStudyDetails study identifier (List of) full details about a specified study
getFeatureList The "DATATYPE_ID" as defined in Demeter(String) which specifies the dataset to be queried List of available feature types with associated value semantics, available in a specified dataset (MOBY namespace)
getOntologyTermDetails The Ontology Term LSID
sample input: urn:lsid:generationcp.org:
OntologyTerm:GCP_200.0000001
The ontology term details

CIRAD

Name of Web Service Input Output
Get_TropGENE_Accession accession information about marker types and locus
getGenomicFeatureDetails genomic feature identifier(with a secondary input precising the type of the genomic feature : locus/qtl) details on this feature (including map positions on all available maps)
getLocusByName a locus or QTL identifier with a possibility of wildcard ('locus' or 'qtl' must be specified in the secondary input) a collection of locus or QTL identifiers.
getMapByName a map identifier with a possibility of wildcard a collection of matching map identifiers
getMapDetails a map identifier details on this map (including map features, length...)
getQTLByOntology a trait term as input (in a GCP_SimpleIdentifier id) a collection of QTL identifiers annotated with this ontology as output
getSequenceByLocus identifier of a locus of TropgeneDB the sequence of the locus and the EMBL accession of the locus (id of the GCP_SimpleSequence)
getGeneByGOTerm gene ontology id or a gene ontology term a list of gene products identifiers
getGeneByKeywords gene product names or description returns a list of identifiers of gene products (protein or RNA)
getGeneWithFST gene product identifier returns FST identifiers
getGermplasmByPhenotype a Trait ontology term or id mutant germplasm annotated with this given ontology
getTropgeneInfoLocus    
getTropgeneLocusSequence    
getTropgeneMapInformation    
getTropgeneQTL    

ICRISAT (to follow)

INIBAP

Name of Web Service Input Output
GetMGISAccessionList a collection of a unique input object related to accessions selection criteria a collection of output objects representing accessions in the MGIS database
Get_TropGENE_Distance_Matrix   returns different kinds of distance matrices built from a complete disjunctive matrix using R
Get_TropGENE_Distance_Matrix_By_Indices   returns different kinds of distance matrices built from a complete disjunctive matrix using R. All these distances are of type d = p1 - s with s a similarity coefficient. (parameter: for instance 1 = Jaccard. for further information see http://cran.r-project.org/ package ade4 method dist.binary)
Get_TropGENE_Nj_Tree   a neighbour joining tree built from a distance matrix using R and creates a file in the NEXUS format

NIAS
Name of Web Service Output
getTranscriptsByOntologyTerm transcripts with specific gene ontology as annotation.
getReportersOfTranscript Reporters of microarray corresponding to a transcript.
getGeneExpressionByReporter expression data on a probe derived from microarray experiment.