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bioMoby
mobyClient
mobyDataTypes
mobyExceptions
mobyMarshal
mobyRegister
mobyService
ontology
AGI_LocusCode
Allele_freq
AminoAcidSequence
B64_encoded_gif
B64_encoded_jpeg
B64_encoded_PDB
B64_Encoded_PNG
B64_Encoded_Postscript
BasicGFFSequenceFeature
ClustalAlnFormattedText
CommentedAASequence
CommentedDNASequence
CommentedRNASequence
DateTime
Decypher_Text
DNASequence
DNASequenceWithGFFFeatures
Edge
EmblFlatfile
FASTA
FASTA_AA
FASTA_NA
GenbankFlatfile
GenericSequence
GeneticElement
Germplasm_Details
Germplasm_List
GFF
GFF1
GFF2
GFF2_5
GFF3
Global_Keyword
GO_Term
Haplotyping_Study_obj
HBond_Pair
HCA_picture
ICIS_Query
ICIS_Query2
ICIS_Query3
IntAct_XML
Interaction
Interaction_partner
InteractionMethod
Interactor
MEME_Text
MGIS_ACCESSION
MMP_Locus
MO_Term_Test
Multi_key_value_pair
MyTree
NCBI_BLAST_Text
NCBI_Blast_XML
NCBI_MEME_Text
NucleotideSequence
PDBFormattedText
PDGJOB
PhenotypeDescription
PubMedMEDLINE
RNASequence
SchematikonMotifID
SchematikonMotifSupport
SchematikonSegmentAttributes
SchematikonSegmentID
SchematikonStructureAnnotation
SchematikonVorocodeName
Scored_acronym_string
Simple_key_value_pair
SimpleAnnotatedGIFImage
SimpleAnnotatedJPEGImage
SINGER_ACCESSION
Snp_allele
Snp_genotype
Study
TargetP_result
TEST
Testout
Text_plain
TextBase64
TextFormatted
TextHtml
TextPlain
TextUuencoded
TextXml
Trait_Details
Tree
TropGENE_ACCESSION
TropGENE_Diversity_Matrix
TropGENE_LOCUS
VirtualSequence
Wildcard_Query
WU_BLAST_Text
webservice
__builtin__.object
:
The most base type
__builtin__.type
:
type(object) -> the object's type type(name, bases, dict) -> a
new type
bioMoby.mobyClient.Central
:
Class Central describes bioMoby Server
bioMoby.mobyClient.Client
:
Implementation of methods that communicate with the bioMoby server
bioMoby.mobyDataTypes.MobyContent
:
The class describes a Moby Content (for queries or answers)
bioMoby.mobyDataTypes.MobyObject
:
Class implementing a bioMoby object
bioMoby.ontology.AGI_LocusCode.MobyAGI_LocusCode
:
Description: Identifier for Arabidopsis Genome Databases
(TAIR,TIGR,MIPS)
(e.g.http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code=At2g17950)
Author: http://mips.gsf.de Contact: Rebecca.Ernst@gsf.de
bioMoby.ontology.BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature
:
Description: An object containing all components necessary to
represent a simple GFF-compliant sequence feature (the content is NOT
validated against the GFF specification) Author: www.illuminae.com
Contact: markw@illuminae.com
bioMoby.ontology.Edge.MobyEdge
:
Description: unstable; under development; subject to redefinition or
deregistration without notice; please do not use Author:
llama.med.harvard.edu Contact: gberriz@hms.harvard.edu
bioMoby.mobyDataTypes.MobyFloat
:
A Float object
bioMoby.ontology.GeneticElement.MobyGeneticElement
:
Description: GeneticElement contains Coordinates Author: mips.gsf.de
Contact: Rebecca.Ernst@gsf.de
bioMoby.ontology.Germplasm_Details.MobyGermplasm_Details
:
Description: Germplasm Information Author: www.iris.irri.org Contact:
mulat@cgiar.org
bioMoby.ontology.Germplasm_List.MobyGermplasm_List
:
Description: ICIS Germplasm List with a particular Property Author:
www.iris.irri.org Contact: mulat@cgiar.org
bioMoby.ontology.Global_Keyword.MobyGlobal_Keyword
:
Description: A namespace for keywords; one keyword only Author:
http://mips.gsf.de Contact: Rebecca.Ernst@gsf.de
bioMoby.ontology.GO_Term.MobyGO_Term
:
Description: A very lightweight object holding a GO term name and its
definition Author: www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.Haplotyping_Study_obj.MobyHaplotyping_Study_obj
:
Description: HapMap related objects Author: www.hapmap.org Contact:
hapmap@hapmap.org
bioMoby.ontology.HBond_Pair.MobyHBond_Pair
:
Description: Pair of residus Author: bioserv.rpbs.jussieu.fr Contact:
rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.ICIS_Query.MobyICIS_Query
:
Description: Text Query for IRIS which allows wildcards Author:
www.iris.irri.org Contact: mulat@cgiar.org
bioMoby.ontology.ICIS_Query2.MobyICIS_Query2
:
Description: Text Query for IRIS with more than one search text.
bioMoby.ontology.ICIS_Query3.MobyICIS_Query3
:
Description: Text Query for IRIS with more than one search text.
bioMoby.mobyDataTypes.MobyInteger
:
An Integer as it is described in the ontology
bioMoby.ontology.Interaction.MobyInteraction
:
Description: An interaction object, in native BioMOBY format.
bioMoby.ontology.Interaction_partner.MobyInteraction_partner
:
Description: unstable; under development; subject to redefinition or
deregistration without notice; please do not use Author:
llama.med.harvard.edu Contact: gberriz@hms.harvard.edu
bioMoby.ontology.InteractionMethod.MobyInteractionMethod
:
Description: We represent an interaction method with this object
Author: pdg.cnb.uam.es Contact: jmfernandez@cnb.uam.es
bioMoby.ontology.Interactor.MobyInteractor
:
Description: An interactor is a reference to an object, with a role
Author: pdg.cnb.uam.es Contact: jmfernandez@cnb.uam.es
bioMoby.ontology.MGIS_ACCESSION.MobyMGIS_ACCESSION
:
Description: Accessions in the MGIS database Author:
biomoby.inibap.org Contact: m.rouard@cgiar.org
bioMoby.ontology.MMP_Locus.MobyMMP_Locus
:
Description: Maize Mapping Project Locus Id Author: www.maizemap.org
Contact: coee@missouri.edu
bioMoby.ontology.MO_Term_Test.MobyMO_Term_Test
:
Description: Test object holding an MO class, individual, class
description and individual description Author: csc.mrc.ac.uk Contact:
derek.fowler@ic.ac.uk
bioMoby.ontology.Multi_key_value_pair.MobyMulti_key_value_pair
:
Description: key/value pair object for key/value pairs with a 1:many
relationship Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.PDGJOB.MobyPDGJOB
:
Description: This object represents a job id, with the answering MOBY
method, killcode, and a timeout Author: pdg.cnb.uam.es Contact:
jmfernandez@cnb.uam.es
bioMoby.ontology.PhenotypeDescription.MobyPhenotypeDescription
:
Description: Object containing a description of the morphological
features of a species Author: http://arabidopsis.info Contact:
beatrice@arabidopsis.info
bioMoby.ontology.SchematikonMotifSupport.MobySchematikonMotifSupport
:
Description: Support and unique support for a Schematikon structure
motif Author: schematikon.org Contact: boris.steipe@utoronto.ca
bioMoby.ontology.SchematikonSegmentAttributes.MobySchematikonSegmentAttributes
:
Description: PDB ID, chain ID, starting amino acid position (chain
position) in the PDB file, insert code, and length for a Schematikon
structure segment -- attributes from a PDB file that uniquely identify a
structure segment in the Schematikon database Author: schematikon.org
Contact: boris.steipe@utoronto.ca
bioMoby.ontology.SchematikonSegmentID.MobySchematikonSegmentID
:
Description: Schematikon protein structure segment ID Author:
schematikon.org Contact: boris.steipe@utoronto.ca
bioMoby.ontology.SchematikonMotifID.MobySchematikonMotifID
:
Description: Schematikon protein structure motif ID Author:
schematikon.org Contact: boris.steipe@utoronto.ca
bioMoby.ontology.SchematikonStructureAnnotation.MobySchematikonStructureAnnotation
:
Description: DSSP, STRIDE, and PROMOTIF annotation for a Schematikon
structure segment / structure motif Author: schematikon.org Contact:
boris.steipe@utoronto.ca
bioMoby.ontology.SchematikonVorocodeName.MobySchematikonVorocodeName
:
Description: Lightweight structural representation of Schematikon
structure motif Author: schematikon.org Contact:
boris.steipe@utoronto.ca
bioMoby.ontology.Scored_acronym_string.MobyScored_acronym_string
:
Description: Any text with a score or ranking associated, with
possible acronym for keyword Author: www.inblosam.com Contact:
michael@inblosam.com
bioMoby.mobyDataTypes.MobySequence
:
An example of sequence as described in the API
bioMoby.ontology.Simple_key_value_pair.MobySimple_key_value_pair
:
Description: Basic key/value pair object for key/value pairs with a
1:1 relationship Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.SINGER_ACCESSION.MobySINGER_ACCESSION
:
Description: Accessions in the SINGER database Author:
singer.grinfo.net Contact: rsood@cgiar.org
bioMoby.mobyDataTypes.MobyString
:
A string as it is described in the ontology
bioMoby.ontology.DateTime.MobyDateTime
:
Description: a date or time in ISO-8601 format Author:
openinformatics.com Contact: jason@openinformatics.com
bioMoby.ontology.Text_plain.MobyText_plain
:
Description: testo plain Author: www.tttd.edu Contact:
tttd@sdsc.edu
bioMoby.ontology.TextBase64.MobyTextBase64
:
Description: base64-encoded data Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.B64_encoded_gif.MobyB64_encoded_gif
:
Description: Base 64 encoded GIF-format image Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.SimpleAnnotatedGIFImage.MobySimpleAnnotatedGIFImage
:
Description: Object containing a GIF image with descriptive text
Author: mips.gsf.de Contact: Rebecca.Ernst@gsf.de
bioMoby.ontology.B64_encoded_jpeg.MobyB64_encoded_jpeg
:
Description: Base 64 encoded JPEG-format image Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.SimpleAnnotatedJPEGImage.MobySimpleAnnotatedJPEGImage
:
Description: An image with descriptive text Author: www.illuminae.com
Contact: markw@illuminae.com
bioMoby.ontology.B64_encoded_PDB.MobyB64_encoded_PDB
:
Description: PDB compressed in zlib and encoded in base 64 Author:
bioserv.rpbs.jussieu.fr Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.B64_Encoded_PNG.MobyB64_Encoded_PNG
:
Description: Base 64 encoded PNG-format image Author:
bioserv.rpbs.jussieu.fr Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.B64_Encoded_Postscript.MobyB64_Encoded_Postscript
:
Description: Base 64 encoded Postscript image Author:
bioserv.rpbs.jussieu.fr Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.HCA_picture.MobyHCA_picture
:
Description: Image produced by HCA Author: bioserv.rpbs.jussieu.fr
Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.TextHtml.MobyTextHtml
:
Description: HTML Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.TextPlain.MobyTextPlain
:
Description: plaintext message Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.TextFormatted.MobyTextFormatted
:
Description: formatted plaintext, where the layout is important to
meaning Author: www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.ClustalAlnFormattedText.MobyClustalAlnFormattedText
:
Description: Clustalw aln format Author: bioserv.rpbs.jussieu.fr
Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.Decypher_Text.MobyDecypher_Text
:
Description: Alignment text output from Decypher hardware search
accelerator Author: coe01.ucalgary.ca Contact:
cheny@coe01.ucalgary.ca
bioMoby.ontology.EmblFlatfile.MobyEmblFlatfile
:
Description: a formatted plaintext EMBL flatfile Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.FASTA.MobyFASTA
:
Description: FASTA formatted sequence Author: www.sdsc.edu Contact:
steube@sdsc.edu
bioMoby.ontology.FASTA_AA.MobyFASTA_AA
:
Description: AA sequence in FASTA format Author:
bioserv.rpbs.jussieu.fr Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.FASTA_NA.MobyFASTA_NA
:
Description: NA sequence in FASTA format Author:
bioserv.rpbs.jussieu.fr Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.GenbankFlatfile.MobyGenbankFlatfile
:
Description: a formatted plaintext genbank flatfile Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.GFF.MobyGFF
:
Description: Generic Feature Format File (of any subtype) Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.GFF1.MobyGFF1
:
Description: Generic Feature Format File type 1 (original Sanger
specification) Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.GFF2.MobyGFF2
:
Description: Generic Feature Format File type 2 (revised Sanger
specification) Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.GFF2_5.MobyGFF2_5
:
Description: Generic Feature Format File type 2.5 (Gbrowse specific
GFF, with special order of column 9) Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.GFF3.MobyGFF3
:
Description: Generic Feature Format File type 3 (SequenceOntology
compliant GFF format) Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.MEME_Text.MobyMEME_Text
:
Description: MEME text output Author: www.sdsc.edu Contact:
steube@sdsc.edu
bioMoby.ontology.MyTree.MobyMyTree
:
Description: Phylogenetic tree Author: www.phytome.org Contact:
dlu@email.unc.edu
bioMoby.ontology.NCBI_BLAST_Text.MobyNCBI_BLAST_Text
:
Description: Plaintext Blast report from NCBI Blast software Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.NCBI_MEME_Text.MobyNCBI_MEME_Text
:
Description: MEME text output Author: www.sdsc.edu Contact:
steube@sdsc.edu
bioMoby.ontology.PDBFormattedText.MobyPDBFormattedText
:
Description: PDB formatted text Author: bioserv.rpbs.jussieu.fr
Contact: rpbs-feedback@ebgm.jussieu.fr
bioMoby.ontology.PubMedMEDLINE.MobyPubMedMEDLINE
:
Description: Pubmed article in MEDLINE display format Author:
http://prometheus.brc.mcw.edu/MOBY/Central Contact:
vnarayan@mcw.edu
bioMoby.ontology.TEST.MobyTEST
:
Description: FASTA formatted sequence Author: www.sdsc.edu Contact:
steube@sdsc.edu
bioMoby.ontology.Tree.MobyTree
:
Description: Phylogenetic tree Author: www.phytome.org Contact:
dlu@email.unc.edu
bioMoby.ontology.TropGENE_Diversity_Matrix.MobyTropGENE_Diversity_Matrix
:
Description: Complete disjunctive tables for diversity analysis :
accessions per row, alleles in column, coded in 0/1 with 2 columns per
allele (one for presence, one for absence) Author: tropgenedb.cirad.fr
Contact: manuel.ruiz@cirad.fr
bioMoby.ontology.WU_BLAST_Text.MobyWU_BLAST_Text
:
Description: Plaintext Blast report from WU-Blast software Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.TextUuencoded.MobyTextUuencoded
:
Description: uuencoded data Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.TextXml.MobyTextXml
:
Description: XML formatted text Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.IntAct_XML.MobyIntAct_XML
:
Description: This is XML based on IntAct XSD Author: pdg.cnb.uam.es
Contact: jmfernandez@cnb.uam.es
bioMoby.ontology.NCBI_Blast_XML.MobyNCBI_Blast_XML
:
Description: XML formatted NCBI Blast report Author: www.illuminae.com
Contact: markw@illuminae.com
bioMoby.ontology.Study.MobyStudy
:
Description: ICIS Germplasm List with a particular Property Author:
www.iris.irri.org Contact: mulat@cgiar.org
bioMoby.ontology.TargetP_result.MobyTargetP_result
:
Description: The results of a TargetP
(http://www.cbs.dtu.dk/services/TargetP/) prediction Author: atidb.org
Contact: sean.walsh@bbsrc.ac.uk
bioMoby.ontology.Testout.MobyTestout
:
Description: Test output object Author: www.iris.irri.org Contact:
mulat@cgiar.org
bioMoby.ontology.Trait_Details.MobyTrait_Details
:
Description: ICIS Property/Trait Information Author: www.iris.irri.org
Contact: mulat@cgiar.org
bioMoby.ontology.TropGENE_ACCESSION.MobyTropGENE_ACCESSION
:
Description: Germplasm accessions in the TropGENE database Author:
tropgenedb.cirad.fr Contact: manuel.ruiz@cirad.fr
bioMoby.ontology.TropGENE_LOCUS.MobyTropGENE_LOCUS
:
Description: Loci in the TropGENE database Author: tropgenedb.cirad.fr
Contact: manuel.ruiz@cirad.fr
bioMoby.ontology.VirtualSequence.MobyVirtualSequence
:
Description: This root of the Sequence object hierarchy carries only
the length of the sequence.
bioMoby.ontology.GenericSequence.MobyGenericSequence
:
Description: Represents any molecule that can be described as a
'Sequence', including nucleotide (DNA, RNA, other), amino acid, or any
other molecule with a sequence.
bioMoby.ontology.AminoAcidSequence.MobyAminoAcidSequence
:
Description: Lightweight representation an amino acid sequence Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.CommentedAASequence.MobyCommentedAASequence
:
Description: Represents a Amino Acid Sequence including a String
(Description).
bioMoby.ontology.NucleotideSequence.MobyNucleotideSequence
:
Description: Lightweight representation of any type of nucleotide
sequence (DNA, RNA, etc) Author: www.illuminae.com Contact:
markw@illuminae.com
bioMoby.ontology.DNASequence.MobyDNASequence
:
Description: Lightweight representation a DNA sequence Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.CommentedDNASequence.MobyCommentedDNASequence
:
Description: Represents a DNA Sequence including a String
(Description).
bioMoby.ontology.DNASequenceWithGFFFeatures.MobyDNASequenceWithGFFFeatures
:
Description: A DNA Sequence including GFF-style features.
bioMoby.ontology.RNASequence.MobyRNASequence
:
Description: Lightweight representation an RNA sequence Author:
www.illuminae.com Contact: markw@illuminae.com
bioMoby.ontology.CommentedRNASequence.MobyCommentedRNASequence
:
Description: Represents a RNA Sequence including a String
(Description).
bioMoby.ontology.Wildcard_Query.MobyWildcard_Query
:
Description: Text Query for IRIS which allows wildcards Author:
www.iris.irri.org Contact: mulat@cgiar.org
bioMoby.mobyDataTypes.MobyXref
:
Describes an Xref
bioMoby.mobyDataTypes.MobyZmPDB
:
WARNING: this class was only used as an example of how to transmit PDB
files! It just compress the file using zlib and encode it in order to
embed PDB in xml tags
bioMoby.mobyDataTypes.Parameter
:
This Object defines a parameter
bioMoby.mobyMarshal.MobyMarshaller
:
Transforms a Moby Object into XML
bioMoby.mobyMarshal.MobyUnmarshaller
:
Transform an XML into a Moby Python Object
bioMoby.mobyRegister.GeneralInformations
:
General informations
bioMoby.mobyRegister.Namespace
:
Name space
bioMoby.mobyRegister.ObjectClass
:
An object's class relationships are described as a set of tuple [
('ISA|HAS|HASA', 'name', 'TYPE'), ...]
bioMoby.mobyService.Service
:
It represents a Moby web service
bioMoby.mobyRegister.ServiceType
:
Service's type
bioMoby.mobyRegister.RegistrationObject
:
A registration object
bioMoby.mobyService.ServiceArticle
:
In a service query, it represents an article
bioMoby.mobyService.ServiceList
:
Class representing a service's list
bioMoby.mobyService.ServiceQuery
:
Solely used in the findService should help us to manage list of
services
bioMoby.mobyService.ServiceSecondary
:
The class represents a parameter for the Service Query Object
bioMoby.ontology.Allele_freq.MobyAllele_freq
:
Description: Allele Frequencey Author: www.hapmap.org Contact:
hapmap@hapmap.edu
bioMoby.ontology.Snp_allele.MobySnp_allele
:
Description: Snp Allele Author: www.hapmap.org Contact:
hapmap@hapmap.edu
bioMoby.ontology.Snp_genotype.MobySnp_genotype
:
Description: Snp Genotypes Author: www.hapmap.org Contact:
hapmap@hapmap.edu
bioMoby.webservice.Dispatcher.AbstractDispatcher
:
Subclass this one to create your own dispatcher class a Dispatcher
class must have a execute method
bioMoby.webservice.Dispatcher.Dispatcher
:
All Queries in the MobyContent Object are splitted and executed
bioMoby.webservice.Dispatcher.SimpleDispatcher
:
A simple dispatcher, without execute method
bioMoby.webservice.Dispatcher.PBSDispatcher
:
Dispatcher for PBS jobs
bioMoby.webservice.Dispatcher.LockedIterator
:
Avoid concurrency on the iterator
bioMoby.webservice.Dispatcher.MultiThread
:
Several threads
bioMoby.webservice.Invocators.GeneralInvocator
:
General class for other invocators
bioMoby.webservice.Invocators.CGIPostInvocator
:
Invokes a CGI script
bioMoby.webservice.Invocators.CGIPostMInvocator
:
Functions for multipart post Directly taken from
http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/146306 Invokes a
CGI script in Post multipart
bioMoby.webservice.Invocators.LocalInvocator
:
Invokes local command
bioMoby.webservice.Invocators.PBSInvocator
:
Invokes a command in a qsub
bioMoby.webservice.Invocators.QsubParameters
exceptions.Exception
:
Common base class for all exceptions.
bioMoby.webservice.Dispatcher.EDispatchError
:
Mistake during the process of a query
bioMoby.mobyExceptions.EInvalidArgument
bioMoby.mobyExceptions.EInvalidType
bioMoby.mobyExceptions.EMethodRetrieveError
bioMoby.mobyExceptions.ENotAWSMethod
bioMoby.mobyExceptions.ETypeMismatch
bioMoby.webservice.Invocators.InvocatorError
:
Error during an invocation of method
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