A MouseAtlas anatomy ontology node name="accession" type="string" description="MouseAtlas anatomy ontology node accession. Examples: EMAP:20, EMAP:1300, et al" name=""group" type="boolean" description="false for component node, true for group node" name="name" type="string" description="node name. Examples: inner cell mass, eye, et al" name="fullPath" type="string" description="full path name of the node, Examples: mouse.embryo.tail, et al" name="primaryPath" type="boolean" description="true means the fullPath is the unique primary path (no group node in the path) while false means any other path (at least one group node in the path)" name="parentAccession" type="string" description="the node's parent's accession" name="stage" type="string" description="stage of the node if it is a timed node or empty if it is a abstract node" name="startStage" type="string" description="start stage of (its/the) abstract node" name="endStage" type="string" description="end stage of (its/the) abstract node" name="symbol" type="string" description="gene symbol" name="name" type="string" description="gene name" name="accession" type="string" description="gene MGI accession" name="name" type="string" name="address" type="string" name="city" type="string" name="postcode" type="string" name="country" type="string" name="tel" type="string" name="fax" type="string" name="url" type="string" name="name" type="string" name="tel" type="string" name="email" type="string" name="organization" type="MAOrganization" name="gene" type="string" name="parentOne" type="string" name="parentTwo" type="string" name="species" type="string" name="strain" type="string" name="sex" type="string" name="wildType" type="boolean" name="mutants" type="array of MAMutant" name="stageMethod" type="string" description="such as TS, dpc" name="stageValue" type="string" description="stage value such as 01, 26" name="name" type="string" name="accession" type="string" name="clearingMethod" type="string" name="embeddingReagent" type="string" name="fixationReagent" type="string" name="gene" type="MAGene" name="signalDetectionMethod" type="string" name="probeNote" type="string" name="specimen" type="MAOrganism" name="specimenNote" type="string" name="specimenType" type="string" description="such as section, wholemount, sectioned wholemount et al" name="experimentID" type="string" name="reporter" type="string" Other linked information of one EMAGE submission name="type" type="string" description="link reason such as the same experiment" name="accession" type="string" name="url" type="string" name="authors" type="string" name="name" type="string" name="volume" type="string" name="issue" type="string" name="year" type="short" name="publisher" type="short" name="authors" type="string" name="title" type="string" name="pages" type="string" name="accession" type="string" description="the accession of the article in the Pub Med database" name="publicationInfo" type="MAPublicationVolume" name="cloneName" type="string" name="templateType" type="string" description="cDNA or genomic" name="regions" type="array of string" description="5'UTR, 3 UTR and/or ORF" name="chemistry" type="string" description="RNA or DNA" name="sequences" type="array of MASequence" name="probe" type="MAProbeISH" name="direction" type="string" description="cDNA or genomic" name="label" type="string" description="if the primary detection reagent (i.e. the probe or antibody) was labelled, it is the identity of this label" name="antibodyType" type="string" name="sequence" type="MASequence" name="label" type="string" description="if the antibody was labelled, it is the identity of this label" name="raisedIn" type="string" name="supplier" type="string" description="antibody supplier name" name="catalogueNo" type="string" description="antibody catalogue number" name="sequence" type="MASequence" name="probe" type="MAAntibody" name="antibodyReagents" type="array of string" name="accession" type="string" name="name" type="string" name="note" type="string" name="accession" type="string" name="name" type="string" name="originType" type="string" description="mouse, cellline or other species" name="sequenceType" type="string" name="cellLine" type="MACellLine" name="organism" type="organism" name="accession" type="string" name="endLoc" type="long" name="endLoc" type="long" name="sequence" type="string" name="person" type="MAPerson" description="person/organisation/group" name="project" type="string" name="reason" type="string" name="accession" type="string" description="EMAGE accession such as EMAGE:10" name="acknowledgements" type="array of MAAcknowledgement" name="stagingQuality" type="string" description="1 for poor, 2 for good and 3 for very good" name="assayQuality" type="string" description="1 for poor, 2 for good and 3 for very good" name="referenceStage" type="string" description="theiler stage" name="status" type="string" description="such as public, editing et al" name="history" type="MAHistory" name="validation" type="string" description="editor or submitter" name="project" type="string" name="authors" type="string" name="investigator" type="MAPerson" name="curator" type="MAPerson" name="links" type="array of MALink" name="publications" type="array of MAPublication" name="experiment" type="MAExperiment" description="its instance type determines whether it is ISH, IHC or Repoter experiment" name="expressionTexts" type="array of MAExpressionText" description="manual ontology annotations" name="comments" type="array of string" Summary of one EMAGE submission name="gene" type="string" description="gene symbol or MGI accession" name="stage" type="string" description="theiler stage value such as 01, 10" name="accession" type="string" description="EMAGE accession such as EMAGE:10" name="stagingQuality" type="string" description="1 for poor, 2 for good and 3 for very good" name="assayQuality" type="string" description="1 for poor, 2 for good and 3 for very good" name="recentHistory" type="string" name="specimenStrain" type="string" name="specimentType" type="string" name="userStage" type="string" description="such as TS14, 12 dpc, 12-13 Somit No. et al" name="experimentType" type="string" description="such as ish, ihc, reporter" name="genotype" type="string" name="probeName" type="string" name="tissueAccession" type="string" description="ontology node accession such as EMAP:987" name="pattern" type="string" description="not applicable, homogeneous, graded, regional, spotted, single cell" name="strength" type="string" description="not examined, not detected, detected, strong, moderate, weak, possible" name="location" type="string" name="notes" type="string" name="accession" type="string" name="resource" type="string" name="type" type="string" name="url" type="string" name="tissueAccession" type="string" description="ontology node accession such as EMAP:987" name="submission" type="array of MASubmissionSummary" type="array of string" description="its element can be node accession, timed node accession, or a string which may be (part of) the name/synonym of some node" type="boolean" description="it is only relevant for non-accession element in the 1st input parameter. true means node name/synonym while false means part of node name/synonym" type="boolean" description="it is only relevant for non-accession element in the 1st input parameter. true means node synonym is cosidered while false means node synonym is excluded"

type="array of string"

type="string" description="empty: root node accession will be returned. valid stage value or name: root timed node accession will be returned. invalid stage: null will be returned"

type="string"

type="string" description="empty: node information will be returned. valid stage value or name: timed node information will be returned. invalid stage: null will be returned" type="string" description="stage value of a Theiler stage such as 01, 24"

type="array of MANodeDetail" description="all (timed) node detail information except the root one"

type="boolean" description="true: include synonym, otherwise, exclude them" type="string" description="start stage value/name. empty means the 1st stage" type="string" description="end stage value/name. empty means the last stage"

type="string"

type="array of string" description="its element can be node accession, timed node accession, or a string which may be (part of) the name/synonym of some node" type="boolean" description="it is only relevant for non-accession element in the 1st input parameter. true means node name/synonym while false means part of node name/synonym" type="boolean" description="it is only relevant for non-accession element in the 1st input parameter. true means node synonym is cosidered while false means node synonym is excluded" type="array of string" description="stage value/name. empty means all stages"

type="array of string"

type="array of Strings" description="a list of all possible stage names in order, such as theiler stage names for mouse"

type="string" description="start stage value/name. empty means the 1st stage" type="string" description="end stage value/name. empty means the last stage"

type="array of string" description="a list of required stage names in order, such as theiler stage names for mouse"

type="array of strig" description="a list of all genes (accession or symbol) which have expression data in the EMAGE database"

type="String" description="EMAGE accession"

type="MASubmission" description="all text information of the EMAGE submission"

type="array of MASubmissionSummary" description="a list of summary information of all EMAGE submissions in the EMAGE database"

type="array of string" description="all EMAGE submission accessions in the EMAGE database"

type="String" description="EMAGE accession"

type="array of MAExpressionText" description="all of ontology annotation of the specific EMAGE submission"

type="array of Strings" description="a list of gene (accesison or symbol). empty means any gene" type="boolean" description="only meaningful if the 1st parameter is not empty. true means match gene string exactly, false means case insensitive and partial match" type="boolean" description="only meaningful if the 1st parameter is not empty. true means to consider gene synonym, false means otherwise" type="array of String" description="a list of ontology term, timed node accession or node accession". empty means any ontology term or node type="boolean" description="only meaningful if the 4th parameter is not empty. true means match ontology string exactly, false means case insensitive and partial match" type="boolean" description="only meaningful if the 4th parameter is not empty. true means to consider ontology synonym, false means otherwise" type="array of string" description="stage value/name. empty means any stage" type="array of string" description="expression strength such as strong, detected et al. empty means any gene expression"

type="array of MASubmissionSummary" description="a list of EMAGE submissions which meet the query conditions"

type="array of Strings" description="a list of gene (accesison or symbol). empty means any gene" type="boolean" description="only meaningful if the 1st parameter is not empty. true means match gene string exactly, false means case insensitive and partial match" type="boolean" description="only meaningful if the 1st parameter is not empty. true means to consider gene synonym, false means otherwise" type="array of string" description="stage value/name. empty means any stage" type="array of string" description="expression strength such as strong, detected et al. empty means any gene expression"

type="array of MATissueQueryResult" description="a list of anatomy node accessions and corresponding EMAGE submissions which are about the specific genes within the specific stage range"

type="array of string" description="all timed nodes in which there are gene expressions