class IBiomarkerFolder(IKnowledgeFolder):
'''Biomarker folder.'''
contains('eke.biomarker.interfaces.IBiomarker',
'eke.biomarker.interfaces.IBiomarkerFolder',
'eke.biomarker.interfaces.IReviewListing')
bmoDataSource = schema.TextLine(
title=_(u'Biomarker-Organ RDF Data Source'),
description=
_(u'URL to a source of RDF data that supplements the RDF data source with biomarker-organ data.'
),
required=True)
bmuDataSource = schema.TextLine(
title=_(u'Biomarker-BioMuta RDF Data Source'),
description=
_(u'URL to a source of RDF data that supplements the RDF data source with biomarker-biomuta data.'
),
required=True)
idDataSource = schema.TextLine(
title=_(u'biomarker id external resource API link'),
description=
_(u'URL to a api that allows querying biomarker ids for links and alternative ids of external resources.'
),
required=True)
dataSummary = schema.TextLine(title=_(u'Biomarker Statistics'),
description=_(u'Biomarker statistics.'),
required=False)
disclaimer = schema.Text(
title=_(u'Disclaimer'),
description=_(
u'Legal disclaimer to display on Biomarker Folder pages.'),
required=False,
)
class IElementalBiomarker(IBiomarker):
'''A single, actual biomarker.'''
biomarkerType = schema.TextLine(
title=_(u'Biomarker Type'),
description=_(
u'The general category, kind, or class of this biomarker.'),
required=False)
class IQualityAssuredObject(Interface):
'''An abstract object that undergoes a quality assurance process.'''
qaState = schema.TextLine(
title=_(u'QA State'),
description=
_(u'The current status with regard to quality assurance of this object.'
),
required=False,
)
class IPhasedObject(Interface):
'''An abstract object that undergoes the standard phases of biomarker research.'''
phase = schema.TextLine(
title=_(u'Phase'),
description=
_(u"The current phase of the biomarker's development with regard to this organ."
),
required=False,
)
class IBiomarkerPanel(IBiomarker):
'''A panel of biomarkers that itself behaves as a single (yet composite) biomarker.'''
members = schema.List(
title=_(u'Member Markers'),
description=_(u'Biomarkers that are a part of this panel'),
required=False,
value_type=schema.Object(
title=_(u'Member Marker'),
description=_(u"A biomarker that's part of a panel."),
schema=IBiomarker))
class IBodySystemStudy(IKnowledgeObject, IResearchedObject):
'''Study-specific information on a biomarker's effects on a single organ.'''
contains('eke.biomarker.interfaces.IStudyStatistics')
protocol = schema.Object(
title=_(u'Study'),
description=
_(u'The study or protocol referenced by specific organ with regard to a biomarker.'
),
required=True,
schema=IProtocol)
decisionRule = schema.Text(
title=_(u'Decision Rule'),
description=_(
u'Details about the decision rule for this body system study'),
required=False,
)
class IBiomarkerBodySystem(IKnowledgeObject, IResearchedObject, IPhasedObject,
IQualityAssuredObject):
'''Research into a biomarker's effects on a single body system.'''
contains('eke.biomarker.interfaces.IBodySystemStudy')
description = schema.Text(
title=_(u'Description'),
description=
_(u'A short summary of the research of a biomarker into a specific organ.'
),
required=False)
performanceComment = schema.Text(
title=_(u'Performance Comment'),
description=
_(u'A short summary of the biomarker performance with respect to a specific organ'
),
required=False)
bodySystem = schema.Object(
title=_(u'Organ'),
description=_(
u'The organ for which the biomarker indicates diseases.'),
required=True,
schema=IBodySystem)
cliaCertification = schema.Bool(
title=_(u'CLIA Certification'),
description=_(
u'True if this biomarker has been certified by CLIA for this organ.'
),
required=False,
default=False,
)
fdaCertification = schema.Bool(
title=_(u'FDA Certification'),
description=
_(u'True if this biomarker has been certified by the FDA for this organ.'
),
required=False,
default=False,
)
class IReviewListing(Interface):
'''A selection of biomarkers that are up for review.'''
title = schema.TextLine(
title=_(u'Title'),
description=_(u'Name of this listing.'),
required=True,
)
description = schema.Text(
title=_(u'Description'),
description=_(u'A short summary of this review listing.'),
required=False,
)
accessGroup = schema.TextLine(
title=_(u'Access Group URI'),
description=
_(u'URI of the access group whose biomarkers should appear in the listing.'
),
required=True,
)
class IResearchedObject(Interface):
'''An abstract object that is researched; that is, there are studies,
publications, datasets, and other resources about it.'''
protocols = schema.List(
title=_(u'Protocols & Studies'),
description=_(u'Protocols and studies that are studying this object.'),
required=False,
value_type=schema.Object(
title=_(u'Study'),
description=_(u'A study or protocol studying an object.'),
schema=IProtocol))
publications = schema.List(
title=_(u'Publications'),
description=_(
u'Publications that have been written talking about this object.'),
required=False,
value_type=schema.Object(
title=_(u'Publication'),
description=_(u'A publication talking about an object.'),
schema=IPublication))
resources = schema.List(
title=_(u'Resources'),
description=_(u'Additional resources about this object.'),
required=False,
value_type=schema.Object(
title=_(u'Resource'),
description=_(u'An additional resource about an object.'),
schema=IKnowledgeObject))
datasets = schema.List(
title=_(u'Datasets'),
description=_(
u'Datasets providing measured scientific bases for this biomarker.'
),
required=False,
value_type=schema.TextLine(
title=_(u'Dataset'),
description=
_(u'Dataset providing a measured scientific basis for this biomarker.'
),
))
from eke.biomarker.interfaces import IBiomarker
from eke.knowledge.content import knowledgeobject
from Products.Archetypes import atapi
from Products.ATContentTypes.content.folder import ATFolder
from Products.CMFCore.utils import getToolByName
from zope.interface import implements, directlyProvides
from zope.schema.interfaces import IVocabularyFactory
from zope.schema.vocabulary import SimpleVocabulary
predicateURIBase = 'http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#'
predicateURIBaseEdrn = 'http://edrn.nci.nih.gov/xml/rdf/edrn.rdf#'
QualityAssuredObjectSchema = atapi.Schema((atapi.StringField(
'qaState',
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(label=_(u'QA State'), ),
predicateURI=predicateURIBase + 'QAState',
), ))
PhasedObjectSchema = atapi.Schema((atapi.StringField(
'phase',
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(label=_(u'Phase'), ),
predicateURI=predicateURIBase + 'Phase',
), ))
ResearchedObjectSchema = atapi.Schema((
atapi.ReferenceField(
'protocols',
storage=atapi.AnnotationStorage(),
enforceVocabulary=True,
from base import Biomarker, QualityAssuredObjectSchema, predicateURIBase
from eke.biomarker import ProjectMessageFactory as _
from eke.biomarker.config import PROJECTNAME
from eke.biomarker.interfaces import IElementalBiomarker
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
ElementalBiomarkerSchema = Biomarker.schema.copy() + QualityAssuredObjectSchema.copy() + atapi.Schema((
atapi.StringField(
'biomarkerType',
storage=atapi.AnnotationStorage(),
required=False,
widget=atapi.StringWidget(
label=_(u'Biomarker Type'),
description=_(u'The general category, kind, or class of this biomarker.'),
),
predicateURI=predicateURIBase + 'Type',
),
))
finalizeATCTSchema(ElementalBiomarkerSchema, folderish=True, moveDiscussion=False)
class ElementalBiomarker(Biomarker):
'''Elemental biomarker.'''
implements(IElementalBiomarker)
schema = ElementalBiomarkerSchema
portal_type = 'Elemental Biomarker'
biomarkerType = atapi.ATFieldProperty('biomarkerType')
qaState = atapi.ATFieldProperty('qaState')
class IStudyStatistics(IKnowledgeObject):
'''Statistician-friendly statistics.'''
sensitivity = schema.Float(
title=_(u'Sensitivity'),
description=_(
u'Proportion of actual positives that are correctly identified.'),
required=False)
specificity = schema.Float(
title=_(u'Specificity'),
description=_(
u'Proportion of actual negatives that are correctly identified.'),
required=False)
npv = schema.Float(
title=_(u'NPV'),
description=_(
u'Ratio of true negatives to combined true and false negatives.'),
required=False)
ppv = schema.Float(
title=_(u'PPV'),
description=_(
u'Ratio of true positives to combined true and false positives.'),
required=False)
prevalence = schema.Float(title=_(u'Prevalence'),
description=_(u'A percentage.'),
required=False)
details = schema.TextLine(
title=_(u'Details'),
description=_(u'Detailed notes about this set of statistics.'),
required=False)
specificAssayType = schema.Text(
title=_(u'Specific Assay Type'),
description=_(u'Information about the specific assay type used'),
required=False)
from base import Biomarker, QualityAssuredObjectSchema, predicateURIBase
from eke.biomarker import ProjectMessageFactory as _
from eke.biomarker.config import PROJECTNAME
from eke.biomarker.interfaces import IElementalBiomarker
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
ElementalBiomarkerSchema = Biomarker.schema.copy(
) + QualityAssuredObjectSchema.copy() + atapi.Schema((atapi.StringField(
'biomarkerType',
storage=atapi.AnnotationStorage(),
required=False,
widget=atapi.StringWidget(
label=_(u'Biomarker Type'),
description=_(
u'The general category, kind, or class of this biomarker.'),
),
predicateURI=predicateURIBase + 'Type',
), ))
finalizeATCTSchema(ElementalBiomarkerSchema,
folderish=True,
moveDiscussion=False)
class ElementalBiomarker(Biomarker):
'''Elemental biomarker.'''
implements(IElementalBiomarker)
schema = ElementalBiomarkerSchema
from eke.biomarker import ProjectMessageFactory as _
from eke.biomarker.config import PROJECTNAME
from eke.biomarker.content.base import predicateURIBase
from eke.biomarker.interfaces import IStudyStatistics
from eke.knowledge.content.knowledgeobject import KnowledgeObject
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
StudyStatisticsSchema = KnowledgeObject.schema.copy() + atapi.Schema((
atapi.FloatField(
'sensitivity',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.DecimalWidget(
label=_(u'Sensitivity'),
description=_(
u'Proportion of actual positives that are correctly identified.'
),
),
predicateURI=predicateURIBase + 'Sensitivity',
),
atapi.FloatField(
'specificity',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.DecimalWidget(
label=_(u'Specificity'),
description=_(
u'Proportion of actual negatives that are correctly identified.'
),
from eke.biomarker.interfaces import IBiomarkerFolder
from eke.biomarker.utils import setFacetedNavigation
from eke.knowledge.content import knowledgefolder
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from Products.CMFCore.utils import getToolByName
from zope.interface import implements
BiomarkerFolderSchema = knowledgefolder.KnowledgeFolderSchema.copy(
) + atapi.Schema((
atapi.StringField(
'bmoDataSource',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Biomarker-Organ RDF Data Source'),
description=
_(u'URL to a source of RDF data that supplements the RDF data source with biomarker-organ data.'
),
size=60,
),
),
atapi.StringField(
'bmuDataSource',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Biomarker-BioMuta RDF Data Source'),
description=
_(u'URL to a source of RDF data that supplements the RDF data source with biomarker-BioMuta data.'
),
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
BiomarkerPanelSchema = Biomarker.schema.copy(
) + QualityAssuredObjectSchema.copy() + atapi.Schema((atapi.ReferenceField(
'members',
enforceVocabulary=True,
multiValued=True,
relationship='panelComposition',
required=False,
storage=atapi.AnnotationStorage(),
vocabulary_display_path_bound=-1,
vocabulary_factory=u'eke.biomarker.BiomarkersVocabulary',
widget=atapi.ReferenceWidget(
label=_(u'Member Markers'),
description=_(u'Biomarkers that are a part of this panel.'),
),
), ))
finalizeATCTSchema(BiomarkerPanelSchema, folderish=True, moveDiscussion=False)
class BiomarkerPanel(Biomarker):
'''Biomarker panel.'''
implements(IBiomarkerPanel)
schema = BiomarkerPanelSchema
portal_type = 'Biomarker Panel'
members = atapi.ATReferenceFieldProperty('members')
qaState = atapi.ATFieldProperty('qaState')
class IBiomarker(IKnowledgeObject, IResearchedObject, IQualityAssuredObject):
'''An abstract biomarker.'''
contains('eke.biomarker.interfaces.IBiomarkerBodySystem')
title = schema.TextLine(title=_(u'Title'),
description=_(u'The main name of the biomarker.'),
required=True)
description = schema.Text(
title=_(u'Description'),
description=_(u'A short summary of the biomarker.'),
required=False)
shortName = schema.TextLine(
title=_(u'Short Name'),
description=_(u'A shorter and preferred alias for the biomarker.'),
required=False)
hgncName = schema.TextLine(
title=_(u'HGNC Name'),
description=_(
u'The name assigned by the HUGO Gene Nomenclature Committee.'),
required=False,
)
bmAliases = schema.List(
title=_(u'Aliases'),
description=_(u'Additional names by which the biomarker is known.'),
required=False,
value_type=schema.TextLine(
title=_(u'Alias'),
description=_(u'Another name for a biomarker.')))
indicatedBodySystems = schema.List(
title=_(u'Indicated Organs'),
description=_(u'Organs for which this biomarker is an indicator.'),
required=False,
value_type=schema.TextLine(
title=_(u'Indicated Organ'),
description=_(u'Organ for which this biomarker is an indicator.')))
accessGroups = schema.List(
title=_(u'Access Groups'),
description=_(u'Groups that are allowed access to this biomarker.'),
required=False,
value_type=schema.TextLine(
title=_(u'Access Group'),
description=_(
u'A single URI identifying a group that may access a biomarker.'
)))
biomarkerKind = schema.TextLine(
title=_(u'Kind'),
description=_(u'What kind of biomarker.'),
required=False,
)
geneName = schema.TextLine(
title=_(u'Gene Symbol/Name'),
description=_(
u'The biomarker annotation that indicates gene symbol or name.'),
required=False,
)
uniProtAC = schema.TextLine(
title=_(u'Uniprot Accession'),
description=
_(u'The biomarker annotation that indicates the associated uniprot accession.'
),
required=False,
)
mutCount = schema.TextLine(
title=_(u'Number of Mutation Sites'),
description=
_(u'The biomarker annotation that indicates the number of mutation sites.'
),
required=False,
)
pmidCount = schema.TextLine(
title=_(u'Pubmed ID Count'),
description=
_(u'The biomarker annotation that indicates the number of associated pubmed ids.'
),
required=False,
)
cancerDOCount = schema.TextLine(
title=_(u'CancerDO Count'),
description=_(
u'The biomarker annotation that indicates the CancerDO.'),
required=False,
)
affProtFuncSiteCount = schema.TextLine(
title=_(u'Affected Protein Function Site Count'),
description=
_(u'The biomarker annotation that indicates the number of affected protein function sites.'
),
required=False,
)
from eke.biomarker.config import PROJECTNAME
from eke.biomarker.interfaces import IBiomarkerFolder
from eke.biomarker.utils import setFacetedNavigation
from eke.knowledge.content import knowledgefolder
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from Products.CMFCore.utils import getToolByName
from zope.interface import implements
BiomarkerFolderSchema = knowledgefolder.KnowledgeFolderSchema.copy() + atapi.Schema((
atapi.StringField(
'bmoDataSource',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Biomarker-Organ RDF Data Source'),
description=_(u'URL to a source of RDF data that supplements the RDF data source with biomarker-organ data.'),
size=60,
),
),
atapi.StringField(
'bmuDataSource',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Biomarker-BioMuta RDF Data Source'),
description=_(u'URL to a source of RDF data that supplements the RDF data source with biomarker-BioMuta data.'),
size=60,
),
),
atapi.StringField(
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
from Products.ATContentTypes.content.folder import ATFolder
BodySystemStudySchema = KnowledgeObject.schema.copy() + ResearchedObjectSchema.copy() + ATFolder.schema.copy() + atapi.Schema((
atapi.ReferenceField(
'protocol',
enforceVocabulary=True,
multiValued=False,
relationship='protocolStudyingBiomarkerThatIndicatesForAnOrgan',
required=True,
storage=atapi.AnnotationStorage(),
vocabulary_display_path_bound=-1,
vocabulary_factory=u'eke.study.ProtocolsVocabulary',
widget=atapi.ReferenceWidget(
label=_(u'Protocol'),
description=_(u'The protocol or study that analyzed the organ for which the biomarker indicates diseases.'),
),
predicateURI=predicateURIBase + 'referencesStudy',
),
atapi.StringField(
'decisionRule',
required=False,
searchable=True,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Decision Rule'),
description=_(u'Details about the decision rule for this study')
),
predicateURI=predicateURIBase + 'DecisionRule',
),
from eke.biomarker import ProjectMessageFactory as _
from eke.biomarker.config import PROJECTNAME
from eke.biomarker.content.base import predicateURIBase
from eke.biomarker.interfaces import IStudyStatistics
from eke.knowledge.content.knowledgeobject import KnowledgeObject
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
StudyStatisticsSchema = KnowledgeObject.schema.copy() + atapi.Schema((
atapi.FloatField(
'sensitivity',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.DecimalWidget(
label=_(u'Sensitivity'),
description=_(u'Proportion of actual positives that are correctly identified.'),
),
predicateURI=predicateURIBase + 'Sensitivity',
),
atapi.FloatField(
'specificity',
required=False,
storage=atapi.AnnotationStorage(),
widget=atapi.DecimalWidget(
label=_(u'Specificity'),
description=_(u'Proportion of actual negatives that are correctly identified.'),
),
predicateURI=predicateURIBase + 'Specificity',
),
atapi.FloatField(
from Products.ATContentTypes.content.folder import ATFolder
from Products.CMFCore.utils import getToolByName
from zope.interface import implements, directlyProvides
from zope.schema.interfaces import IVocabularyFactory
from zope.schema.vocabulary import SimpleVocabulary
predicateURIBase = 'http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#'
predicateURIBaseEdrn = 'http://edrn.nci.nih.gov/xml/rdf/edrn.rdf#'
QualityAssuredObjectSchema = atapi.Schema((
atapi.StringField(
'qaState',
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'QA State'),
),
predicateURI=predicateURIBase + 'QAState',
),
))
PhasedObjectSchema = atapi.Schema((
atapi.StringField(
'phase',
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Phase'),
),
from zope.interface import implements
from Products.ATContentTypes.content.folder import ATFolder
BodySystemStudySchema = KnowledgeObject.schema.copy(
) + ResearchedObjectSchema.copy() + ATFolder.schema.copy() + atapi.Schema((
atapi.ReferenceField(
'protocol',
enforceVocabulary=True,
multiValued=False,
relationship='protocolStudyingBiomarkerThatIndicatesForAnOrgan',
required=True,
storage=atapi.AnnotationStorage(),
vocabulary_display_path_bound=-1,
vocabulary_factory=u'eke.study.ProtocolsVocabulary',
widget=atapi.ReferenceWidget(
label=_(u'Protocol'),
description=
_(u'The protocol or study that analyzed the organ for which the biomarker indicates diseases.'
),
),
predicateURI=predicateURIBase + 'referencesStudy',
),
atapi.StringField(
'decisionRule',
required=False,
searchable=True,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Decision Rule'),
description=_(u'Details about the decision rule for this study')),
predicateURI=predicateURIBase + 'DecisionRule',
from Products.Archetypes import atapi
from Products.ATContentTypes.content.schemata import finalizeATCTSchema
from zope.interface import implements
BiomarkerPanelSchema = Biomarker.schema.copy() + QualityAssuredObjectSchema.copy() + atapi.Schema((
atapi.ReferenceField(
'members',
enforceVocabulary=True,
multiValued=True,
relationship='panelComposition',
required=False,
storage=atapi.AnnotationStorage(),
vocabulary_display_path_bound=-1,
vocabulary_factory=u'eke.biomarker.BiomarkersVocabulary',
widget=atapi.ReferenceWidget(
label=_(u'Member Markers'),
description=_(u'Biomarkers that are a part of this panel.'),
),
),
))
finalizeATCTSchema(BiomarkerPanelSchema, folderish=True, moveDiscussion=False)
class BiomarkerPanel(Biomarker):
'''Biomarker panel.'''
implements(IBiomarkerPanel)
schema = BiomarkerPanelSchema
portal_type = 'Biomarker Panel'
members = atapi.ATReferenceFieldProperty('members')
qaState = atapi.ATFieldProperty('qaState')
from Products.ATContentTypes.content.folder import ATFolder
from zope.interface import implements
BiomarkerBodySystemSchema = KnowledgeObject.schema.copy() + QualityAssuredObjectSchema.copy() + PhasedObjectSchema.copy() \
+ ResearchedObjectSchema.copy() + ATFolder.schema.copy() + atapi.Schema((
atapi.ReferenceField(
'bodySystem',
enforceVocabulary=True,
multiValued=False,
relationship='bodySystemIndicatesFor',
required=True,
storage=atapi.AnnotationStorage(),
vocabulary_display_path_bound=-1,
vocabulary_factory=u'eke.knowledge.BodySystems',
widget=atapi.ReferenceWidget(
label=_(u'Organ'),
description=_(u'The organ for which the biomarker indicates diseases.'),
),
# No predicateURI here; the RDF output just names the organ, so we'll have to
# link it manually during ingest.
),
atapi.StringField(
'performanceComment',
required=False,
searchable=True,
storage=atapi.AnnotationStorage(),
widget=atapi.StringWidget(
label=_(u'Performance Comment'),
description=_(u'A description of biomarker performance with respect to this organ'),
),
predicateURI='http://edrn.nci.nih.gov/rdf/rdfs/bmdb-1.0.0#PerformanceComment',