ambit2.base.data

Class SubstanceRecord

java.lang.Object

ambit2.base.data.StructureRecord

ambit2.base.data.SubstanceRecord

All Implemented Interfaces:

IChemical, IStructureRecord, Serializable

public class SubstanceRecord
extends StructureRecord

Same as the parent class, but with related structures

Author:

nina

 {
     "substance": [
         {
             "URI": "http://host:8080/data/substance/IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734",
             "ownerUUID": "IUC4-44bf02d8-47c5-385d-b203-9a8f315911cb",
             "ownerName": "OECD / Paris / France",
             "i5uuid": "IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734",
             "name": "formaldehyde (IUC4 DSN 52)",
             "publicname": "",
             "format": "i5._5.",
             "substanceType": "Existing Chemical",
             "referenceSubstance": {
                 "i5uuid": "ECB5-053aa8c4-d29b-4aa5-b457-5cc3b47f7d8b",
                 "uri": "http://apps.ideaconsult.net:8080/data/query/compound/search/all?search=ECB5-053aa8c4-d29b-4aa5-b457-5cc3b47f7d8b"
             },
             "composition": [],
             "externalIdentifiers": [
                 {
                     "type": "IUCLID4",
                     "id": "DSN 52"
                 }
             ]
         },
         {
             "URI": "http://host:8080/enanomapper/substance/NWKI-71060af4-1613-35cf-95ee-2a039be0388a",
             "ownerUUID": "NWKI-9f4e86d0-c85d-3e83-8249-a856659087da",
             "ownerName": "NanoWiki",
             "i5uuid": "NWKI-71060af4-1613-35cf-95ee-2a039be0388a",
             "name": "Kim2012 NM1",
             "publicname": "CuO",
             "format": "",
             "substanceType": "MetalOxide",
             "referenceSubstance": {
                 "i5uuid": "NWKI-71060af4-1613-35cf-95ee-2a039be0388a",
                 "uri": "http://host:8080/enanomapper/query/compound/search/all?search=NWKI-71060af4-1613-35cf-95ee-2a039be0388a"
             },
             "composition": [],
             "externalIdentifiers": [
                 {
                     "type": "Composition",
                     "id": "CuO"
                 },
                 {
                     "type": "DATASET",
                     "id": "NanoWiki"
                 },
                 {
                     "type": "Has_Identifier",
                     "id": "139"
                 }
             ]
         }
     ]
 }
 

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SubstanceRecord.jsonSubstance

Nested classes/interfaces inherited from interface ambit2.base.interfaces.IStructureRecord

IStructureRecord.MOL_TYPE, IStructureRecord.STRUC_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
protected List<ExternalIdentifier>	externalids
protected int	idsubstance
protected String	internalName
protected String	internalUUID
protected List<ProtocolApplication>	measurements
protected String	ownerName
protected String	ownerUUID
protected String	publicName
protected String	refsubstance_uuid
protected List<CompositionRelation>	relatedStructures
protected String	substancetype

Fields inherited from class ambit2.base.data.StructureRecord

content, dataEntryID, facets, format, formula, id_srcdataset, idchemical, idstructure, inchi, inchiKey, preferedStructure, properties, reference, selected, smiles, type

Constructor Summary

Constructors

Constructor and Description
SubstanceRecord()
SubstanceRecord(int idsubstance)
SubstanceRecord(String uuid)

Method Summary

Modifier and Type	Method and Description
void	addMeasurement(ProtocolApplication measurement)
void	addStructureRelation(CompositionRelation relation)
IStructureRelation	addStructureRelation(String compositionUUID, IStructureRecord record, STRUCTURE_RELATION relation, Proportion value)
void	clear()
List<ExternalIdentifier>	getExternalids()
int	getIdsubstance()
List<ProtocolApplication>	getMeasurements()
String	getOwnerName() Name of the company, which is the substance owner (usually the substance manufacturer)
String	getOwnerUUID() UUID of the company, which is the substance owner (usually the substance manufacturer)
String	getPublicName() Public name of the substance
String	getReferenceSubstanceUUID() referenceSubstance (link to reference structure).Typical use IStructureRecord
List<CompositionRelation>	getRelatedStructures() CompositionRelation
String	getSubstanceName() Substance name, as assigned by the owner
String	getSubstancetype() IUCLID5: monoconsituent, multiconstituent, UVCB (Unknown or Variable composition, Complex reaction products or Biological materials) http://echa .europa.eu/documents/10162/13643/nutshell_guidance_substance_en.pdf
String	getSubstanceUUID() Substance UUID, as assigned by the owner
static String	getURI(String ref, SubstanceRecord item)
void	setExternalids(List<ExternalIdentifier> externalids)
void	setIdsubstance(int idsubstance)
void	setMeasurements(List<ProtocolApplication> measurements)
void	setOwnerName(String ownerName)
void	setOwnerUUID(String ownerUUID)
void	setPublicName(String publicname)
void	setReferenceSubstanceUUID(String uuid)
void	setRelatedStructures(List<CompositionRelation> relatedStructures)
void	setSubstanceName(String internalName) Substance name, as assigned by the owner
void	setSubstancetype(String substancetype)
void	setSubstanceUUID(String internalUUID) Substance UUID as assigned by the substance owner
String	toJSON(String baseReference)
String	toString()

Methods inherited from class ambit2.base.data.StructureRecord

addFacet, addRecordProperties, clearFacets, clearProperties, clone, createProperties, getContent, getDataEntryID, getDatasetID, getFacets, getFormat, getFormula, getIdchemical, getIdstructure, getInchi, getInchiKey, getMap, getNumberOfProperties, getRecordProperties, getRecordProperty, getReference, getSmiles, getType, getWritableContent, isSelected, removeFacet, removeRecordProperty, setContent, setDataEntryID, setDatasetID, setFormat, setFormula, setIdchemical, setIdstructure, setInchi, setInchiKey, setRecordProperty, setReference, setSelected, setSmiles, setType, setUsePreferedStructure, usePreferedStructure

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

externalids

protected List<ExternalIdentifier> externalids

ownerUUID

protected String ownerUUID

ownerName

protected String ownerName

idsubstance

protected int idsubstance

substancetype

protected String substancetype

internalName

protected String internalName

publicName

protected String publicName

internalUUID

protected String internalUUID

refsubstance_uuid

protected String refsubstance_uuid

measurements

protected List<ProtocolApplication> measurements

relatedStructures

protected List<CompositionRelation> relatedStructures

Constructor Detail

SubstanceRecord

public SubstanceRecord()

SubstanceRecord

public SubstanceRecord(String uuid)

SubstanceRecord

public SubstanceRecord(int idsubstance)

Method Detail

getMeasurements

public List<ProtocolApplication> getMeasurements()

setMeasurements

public void setMeasurements(List<ProtocolApplication> measurements)

addMeasurement

public void addMeasurement(ProtocolApplication measurement)

getSubstancetype

public String getSubstancetype()

IUCLID5: monoconsituent, multiconstituent, UVCB (Unknown or Variable composition, Complex reaction products or Biological materials) http://echa .europa.eu/documents/10162/13643/nutshell_guidance_substance_en.pdf

 "substanceType": "Existing Chemical"
 

To be extended for nanomaterials.

Returns:

getSubstanceName

public String getSubstanceName()

Substance name, as assigned by the owner

                "i5uuid": "IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734",
                "name": "formaldehyde (IUC4 DSN 52)",
 

Returns:

setSubstanceName

public void setSubstanceName(String internalName)

Substance name, as assigned by the owner

Parameters:

companyName -

getPublicName

public String getPublicName()

Public name of the substance

Returns:

setPublicName

public void setPublicName(String publicname)

getSubstanceUUID

public String getSubstanceUUID()

Substance UUID, as assigned by the owner

        "i5uuid": "IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734",
        "name": "formaldehyde (IUC4 DSN 52)",
 

Returns:

setSubstanceUUID

public void setSubstanceUUID(String internalUUID)

Substance UUID as assigned by the substance owner

Parameters:

internalUUID -

setSubstancetype

public void setSubstancetype(String substancetype)

getRelatedStructures

public List<CompositionRelation> getRelatedStructures()

CompositionRelation

        "composition": []
 

setRelatedStructures

public void setRelatedStructures(List<CompositionRelation> relatedStructures)

addStructureRelation

public void addStructureRelation(CompositionRelation relation)

addStructureRelation

public IStructureRelation addStructureRelation(String compositionUUID,
                                               IStructureRecord record,
                                               STRUCTURE_RELATION relation,
                                               Proportion value)

getIdsubstance

public int getIdsubstance()

setIdsubstance

public void setIdsubstance(int idsubstance)

setReferenceSubstanceUUID

public void setReferenceSubstanceUUID(String uuid)

getReferenceSubstanceUUID

public String getReferenceSubstanceUUID()

referenceSubstance (link to reference structure).Typical use IStructureRecord

Returns:

clear

public void clear()

Specified by:

clear in interface IStructureRecord

Overrides:

clear in class StructureRecord

toString

public String toString()

Overrides:

toString in class StructureRecord

getOwnerUUID

public String getOwnerUUID()

UUID of the company, which is the substance owner (usually the substance manufacturer)

             "ownerUUID": "IUC4-44bf02d8-47c5-385d-b203-9a8f315911cb",
             "ownerName": "OECD / Paris / France",
 

Returns:

setOwnerUUID

public void setOwnerUUID(String ownerUUID)

getOwnerName

public String getOwnerName()

Name of the company, which is the substance owner (usually the substance manufacturer)

             "ownerUUID": "IUC4-44bf02d8-47c5-385d-b203-9a8f315911cb",
             "ownerName": "OECD / Paris / France",
 

Returns:

setOwnerName

public void setOwnerName(String ownerName)

getExternalids

public List<ExternalIdentifier> getExternalids()

setExternalids

public void setExternalids(List<ExternalIdentifier> externalids)

toJSON

public String toJSON(String baseReference)

getURI

public static String getURI(String ref,
                            SubstanceRecord item)