INOH Pathway Database

INOH Web API Manual

The INOH database provides Simple Object Access Protocol (SOAP) web service APIs. A user who wants to programmatically access INOH pathway data (INOH XML format) can do a keyword search and pathway retrieval search (searchPreviousEvents, searchFollowingEvents, searchController/ControlledEvents, searchHomologousEvents, searchMolecularVariation, searchParentEvent, searchChildEvents) by using these APIs. Users can access the services through programming languages such as Perl, Python, Ruby, and Java.

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INOH Web API list

GID: diagram node id. (e.g. TGF beta super family signaling pathway --> II0000028)
LID: local id in the diagram node. (e.g. TGF beta super family protein --> id1).
MatID: the objects with the same states are assigned the same id in all diagrams. (e.g.TGF beta super family protein --> MI0021214)
INOH Diagram File Format
INOH attribute rules

API	Parameter
Summary & Sample
getDiagram	param0 = GID
get xml file (INOH format) of the GID's diagram. http://www.inoh.org/axis2/services/InohWebService2/getDiagram?param0=II0000028 This sample: get xml file of "TGF beta super family signaling pathway".
getDiagramDisplayName	param0 = GID or GID+ ":" + LID
get diagram name of the object(diagram, node, or edge). http://www.inoh.org/axis2/services/InohWebService2/getDiagramDisplayName?param0=II0000028 This sample: get diagram name of "TGF beta super family signaling pathway".
getDiagramDisplayNames	param0 = array of the GID or GID+ ":" + LID
get all diagram names of the objects(diagram, node, or edge). http://www.inoh.org/axis2/services/InohWebService2/getDiagramDisplayNames?param0=II0000028&param0=II0000002 This sample: get diagram name of "TGF beta super family signaling pathway" and "TGF beta BMP Diagram(MolecularVariation) pathway".
getDiagramIDsAll	N/A
get all diagram ids. http://www.inoh.org/axis2/services/InohWebService2/getDiagramIDsAll
getDiagramNode	param0 = GID+ ":" + LID, param1 = 1 or 0 1: retrieve including the descendant 0: not retrieve including the descendant
get xml file (INOH format) of the id's node object. http://www.inoh.org/axis2/services/InohWebService2/getDiagramNode?param0=II0000028:id663033270&param1=0 This sample: get xml file of "TGF-beta_super_family_signaling_pathway(canonical)" event.
getDiagramNodeID	param0 = GID
get the diagram node id (GID + ":" + LID + ":" + MatID). http://www.inoh.org/axis2/services/InohWebService2/getDiagramNodeID?param0=II0000028
getDiagramNodeIDs	param0 = array of GID
get all the diagram node ids (GID + ":" + LID + ":" + MatID). http://www.inoh.org/axis2/services/InohWebService2/getDiagramNodeIDs?param0=II0000028&param0=II0000029
getEdgeType	param0 = GID + ":" + LID
get edge type. http://www.inoh.org/axis2/services/InohWebService2/getEdgeType?param0=II0000028:id241 This sample: Catalyze edge (II0000028:id241)
getGIDLIDsFromMatID	param0 = MatID
get the GID + ":" + LID from the MatID's object http://www.inoh.org/axis2/services/InohWebService2/getGIDLIDsFromMatID?param0=MI0031892
getGIDsFromMatID	param0 = MatID
get all GIDs of the MatID's object. http://www.inoh.org/axis2/services/InohWebService2/getGIDsFromMatID?param0=MI0015899 This sample: get all diagram ids having "Wnt protein(MatID:MI0015899)".
getNodeDisplayName	param0 = GID + ":" + LID
get the display name. http://www.inoh.org/axis2/services/InohWebService2/getNodeDisplayName?param0=II0000031:id1060086333 This sample: the "Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) event (II0000031:id1060086333)".
getNodeDisplayNames	param0 = array of the GID + ":" + LID
get all the displaynames. http://www.inoh.org/axis2/services/InohWebService2/getNodeDisplayNames?param0=II0000031:id286001069&param0=II0000031:id1297705331&param0=II0000031:id2098695283 This sample: "Wnt protein (II0000031:id286001069)", "Frizzled protein (II0000031:id1297705331)", "Arrow/LRP5/6 protein (II0000031:id2098695283)".
getNodeType	param0 = GID + ":" + LID
get node type. http://www.inoh.org/axis2/services/InohWebService2/getNodeType?param0=II0000031:id1060086333 This sample: "Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) event (II0000031:id1060086333)".
searchBonding	param0 = GID + ":" + LID
get the bonding partner. http://www.inoh.org/axis2/services/InohWebService2/searchBonding?param0=II0000005:id710267271 This sample: search the bonding partner of "EGFR (II0000005:id710267271)".
searchByEdge	param0 = type of edge ("IN","OUT", "Control","Catalyze", "Connected", "PASSING","Identical", "HomologousEvent", "MolecularVariation") , param1 = 0 or 1 or 2 ( 0:EDGE_DIRECTION_BOTH, 1: EDGE_DIRECTION_SOURCE, 2: EDGE_DIRECTION_TARGET) param2 = GID + ":" + LID
search edge. http://www.inoh.org/axis2/services/InohWebService2/searchByEdge?param0=Connected&param1=0&param2=II0000005:id710267271 This sample: search the "Connected edge" between "EGFR(II0000005:id710267271)" protein and "Grb2(II0000005:id1117791053)" protein.
searchChildEvents	param0 = type of node ("EventCompound","Event") param1 = GID + ":" + LID param2 = 1 or 0 1: retrieve it including the descendant 0: not retrieve it including the descendant
search the child events. http://www.inoh.org/axis2/services/InohWebService2/searchChildEvents?param0=EventCompound&param1=II0000028:id663033270&param2=1 This sample: search child events of "TGF-beta_super_family_signaling_pathway(canonical) (II0000028:id663033270)" event.
searchChildNodes	param0 = type of node("Protein","ChemicalSubstance", "MolecularComplex","DNA", "RNA,"Terminal", "Process","Event", "MolecularComplexCompound", "DNACompound", "EventCompound", "EventRelation"), param1 = GID + ":" + LID
get the child nodes. http://www.inoh.org/axis2/services/InohWebService2/searchChildNodes?param0=Protein&param1=II0000031:id1060086333 This sample: search child nodes of the "Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) event (II0000031:id1060086333)".
searchNodeByKeyword	param0 = array of node type ("Protein","ChemicalSubstance", "MolecularComplex","DNA", "RNA,"Terminal", "Process","Event", "MolecularComplexCompound", "DNACompound", "EventCompound", "EventRelation"), param1 = array of attribute type("DisplayName", "Organism", "Evidence", "MoleculeRoleOntology", "EventOntology", "ProcessOntology", "LocationOntology", "GenomeSequenceOntology", "EventRelationOntology", "Comment", "Type", "ExternalReference", "StoichiometricCoefficient", "SequenceFeature", "GeneProduct", "OriginalMaterial"), param2 = array of keyword, param3 = 0 or 1or 2 or 3, 0: exact match, 1: contains, 2:Start with, 3.Ends with, param4 = Ignore case(1:true 0:false), param5 = and/or(1:and, 0:or)
keyword search http://www.inoh.org/axis2/services/InohWebService2/searchNodeByKeyword?param0=Protein&param1=SequenceFeature&param2=phosphorylated&param3=1&param4=1&param5=1 This sample: search "Protein" nodes is annotated "phosphorylated" on "SequenceFeature" property.
searchOntologyRelatedXML	param0 = GID + ":" + LID
search the same ontology objects http://www.inoh.org/axis2/services/InohWebService2/searchOntologyRelatedXML?param0=II0000031:id1060086333 This sample: search all the events that whose EventOntology property is "IEV_0001949:Binding of Wnt, Frizzled and Arrow/LRP5/6 in extracellula". II0000031:id1060086333 --> Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) event. --> EventOntology: IEV_0001949:Binding of Wnt, Frizzled and Arrow/LRP5/6 in extracellula)
searchParentEvent	param0 = GID + ":" + LID
search parent events. http://www.inoh.org/axis2/services/InohWebService2/searchParentEvent?param0=II0000031:id286001069 This sample: search the parent event of the "Wnt protein(II0000031:id286001069)".
searchParentEvents	param0 = array of GID + ":" + LID
search parent events. http://www.inoh.org/axis2/services/InohWebService2/searchParentEvents?param0=II0000005:id43049120&param0=II0000006:id1248678234 This sample: search the parent event of "EGF protein (II0000005:id43049120)" and "FGF protein (II0000006:id1248678234)".
searchParentNode	param0 = GID + ":" + LID
search the parent node. http://www.inoh.org/axis2/services/InohWebService2/searchParentNode?param0=II0000005:id179958873 This sample: search the parent node of the "ERK cascade (EGF pathway) event (II0000005:id179958873)".
searchPreviousEventsCuratedAndInferredXML	param0 = GID + ":" + LID param1 = pathway depth (integer)
search "Curated" and "Inferred" event of the previous events. http://www.inoh.org/axis2/services/InohWebService2/searchPreviousEventsCuratedAndInferredXML?param0=II0000002:id750656793&param1=3 This sample: search the "Curated" and "Inferred" previous event of "Nuclear import of Smad1:Smad4 event (II0000002:id750656793).
searchPreviouEventsCuratedXML	param0 = GID + ":" + LID param1 = pathway depth (integer)
search "Curated" event of the previous events. http://www.inoh.org/axis2/services/InohWebService2/searchPreviousEventsCuratedXML?param0=II0000002:id750656793&param1=3 This sample: search the "Curated" previous event of "Nuclear import of Smad1:Smad4" event (II0000031:id1060086333).
searchPreviousEventsInferredXML	param0 = GID + ":" + LID, param1 = pathway depth (integer)
search "Inffered" event xml of the previous events. http://www.inoh.org/axis2/services/InohWebService2/searchPreviousEventsInferredXML?param0=param0=II0000031:id1060086333&param1=3 This sample: search the "Inferred" previous event of "Nuclear import of Smad1:Smad4 event (II0000031:id1060086333).
searchFollowEventsCuratedAndInferredXML	param0 = GID + ":" + LID param1 = pathway depth (integer)
search the "Curated" and "Inferred" following events. http://www.inoh.org/axis2/services/InohWebService2/searchFollowEventsCuratedAndInferredXML?param0=II0000002:id750656793&param1=3 This sample: search the "Curated" and "Inferred" following events of "Nuclear import of Smad1:Smad4 event (II0000002:id750656793)".
searchFollowingEventsCuratedXML	param0 = GID + ":" + LID param1 = pathway depth (integer)
search the "Curated" following events. http://www.inoh.org/axis2/services/InohWebService2/searchFollowingEventsCuratedXML?param0=II0000002:id750656793&param1=3 This sample: search the "Curated" following event of "Nuclear import of Smad1:Smad4" event (II0000002:id750656793).
searchFollowingEventsInferredXML	param0 = GID + ":" + LID, param1 = pathway depth (integer)
search "Inffered" event of the following events. http://www.inoh.org/axis2/services/InohWebService2/searchFollowingEventsInferredXML?param0=II0000002:id750656793&param1=3 This sample: search the "Inferred" following event of "Nuclear import of Smad1:Smad4 event (II0000002:id750656793).
searchControllerEventsAndControlledEventsXML	param0 = GID + ":" + LID
search the pair of the controller event and controlled event. http://www.inoh.org/axis2/services/InohWebService2/searchControllerEventsAndControlledEventsXML?param0=II0000028:id1889369972 This sample: search the controller and controlled events of the "Binding of R-smad:smad4 complex, Corepressor, Deacetylase and responsive element event (II0000028:id1889369972)".
searchControllerEventsXML	param0 = GID + ":" + LID
search the controller event. http://www.inoh.org/axis2/services/InohWebService2/searchControllerEventsXML?param0=II0000031:id1060086333 This sample: search the controller events of the "Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) event (II0000031:id1060086333)".
searchControlledEventsXML	param0 = GID + ":" + LID
search the controlled events. http://www.inoh.org/axis2/services/InohWebService2/searchControlledEventsXML?param0=II0000031:id220965320 This sample: search the controlled events of the "Binding of Wnt and HSPG (Canonical) event (II0000031:id220965320).
searchSuperEventAndSubEventsXML	param0 = GID + ":" + LID
search the super and sub events. http://www.inoh.org/axis2/services/InohWebService2/searchSuperEventAndSubEventsXML?param0=II0000028:id372437128 This sample: search the super and sub events of the "Gene expression of smad7 by R-smad:smad4 event (II0000028:id372437128)".
searchSuperEventXML	param0 = GID + ":" + LID
search the super events. http://www.inoh.org/axis2/services/InohWebService2/searchSuperEventXML?param0=II0000023:id1974835916 This sample: search the super event of the "Negative feedback regulation of JAK STAT pathway by (cytokine receptor degradation signaling) event (II0000023:id1974835916)".
searchSubEventsXML	param0 = GID + ":" + LID
search the sub events. http://www.inoh.org/axis2/services/InohWebService2/searchSubEventsXML?param0=II0000002:id999443139 This sample: search the sub events of the "BMP2 signaling pathway(through Smad) event (II0000002:id999443139)".
search the homologous events. http://www.inoh.org/axis2/services/InohWebService2/searchHomologousEventsXML?param0=II0000031:id1060086333 This sample: search the homologous events of "Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) event (II0000031:id1060086333)".
search the "molecular variation" events. http://www.inoh.org/axis2/services/InohWebService2/searchMolecularVariationXML?param0=II0000023:id161744955 This sample: search the "molecular variation" events of "Binding of cytokine and cytokine receptors and conformational change of receptors event (II0000023:id161744955)".
searchPathwayRetrievalXML	param0 = GID + ":" + LID, param1 = pathway depth (integer)
all "pathway retrieval search". http://www.inoh.org/axis2/services/InohWebService2/searchPathwayRetrievalXML?param0=II0000031:id1060086333&param1=3 This sample: all "pathway retrieval search" about "Binding of Wnt, Frizzled and Arrow/LRP5/6 (Canonical) (II0000031:id106008633)".
searchSameEvents	param0 = GID + ":" + LID
search other event connected by "Identical edge" http://www.inoh.org/axis2/services/InohWebService2/searchSameEvents?param0=II0000036:id1552625225 This sample: "nuclear translocation of JNK (II0000036:id1552625225)".
searchSameMaterials	param0 = GID + ":" + LID
search the same ontology materials. http://www.inoh.org/axis2/services/InohWebService2/searchSameMaterials?param0=II0000102:id815693559 This sample: search the materials that MoleculeRoleOntology is "IMR_0000052:insulin". II0000102:id815693559 --> insulin A protein --> MoleculeRoleOntology: IMR_0000052:insulin
searchDiagram	param0 = GID + ":" + LID
get GID. http://www.inoh.org/axis2/services/InohWebService2/searchDiagram?param0=II0000005:id2016660283 This sample: get GID of the "EGF signaling pathway (D. melanogaster) event (II0000005:id2016660283)".
getDiagramEdge	GID+ ":" + LID
get xml file of the ID's edge object. http://www.inoh.org/axis2/services/InohWebService2/getDiagramEdge?param0=II0000044:id470715347
getVersion	N/A
get the version of INOH server. http://www.inoh.org/axis2/services/InohWebService2/getVersion