= OmicsConnect wiki =

This page reports current issues and plans with omicsconnect, an extension on top of Observ.
This work is in the context of EU-BioSHARE WP4.

NB this document formatted in trac wiki format, so we can include it online. Syntax:
* unsolved issues
* ~~ solved issues ~~
>> comments

== showstoppers ==

* mrefs master/detail forms don't behave well. Examples:
	* adding new citations for study.
	* adding new measurement to protocol 
	
== discussion items ==

* Phenotype method <-> protocol / measurement
* Who does contribution: Person or an PersonAffiliation?	

== WormQTL datatypes review ==
'''v1 -> v2: notes'''
* analysis -> computeprotocol: needs merging work
* derivedtrait -> MISSING: observablefeature is what you want, but this needs to be typed in some way
* parameterset -> mref 'parameters' in computeprotocol: look into consequences not having sets for this
* binarydatamatrix -> MISSING: matrix backend specific, link to binary storage files
* gene -> MISSING: probably sequencecharacteristic? how is this typed? must be subclassed first? fields such as xref to Chromosome, bp location, etc via sequencerelation?
* parametervalue -> computeparameter: better than before with datatyping/freerange values
* chromosome -> chromosome: missing some handy fields such as 'orderNr' and 'isAutosomal' ('rank' in sequencerelation?)
* investigation -> study: OK
* probe -> [see: gene]
* data -> dataset: might need some extra fields such as ValueType, ColumnType, RowType, Storage, etc
* marker -> marker: missing some fields: xref to Chromosome, cM location, reportsFor. 'seqlength' as int might be too small? (2x10^9 when signed)
* runtimeproperty -> MISSING: but make molgenis-wide build-in?
* dataname  -> computeparameter: if values can be proper XREFs
* measurement -> [see: derivedtrait]
* sample -> MISSING: subclass of observationtarget?
* dataset -> [see: parameterset, if values can be proper XREFs]
* panel -> panel: OK
* snp -> [see: gene]
* datavalue -> computeparameter: if values can be proper XREFs
* parametername -> computeparameter: OK
* transcript -> [see: gene]
* investigationfile -> MISSING: but debatable use/implementation

== wanted entities ==

Domain model:

'''observation'''
* Characteristic: 'is a' or 'has a' statements about an object
* ObservableFeature: characteristic observed (is/has) or question asked (what is?)
	* Measurement: feature defined by description, unit, dataType, permittedValue
	* PermittedValue: a categorical value state for Measurement 
* ObservationTarget: target of observation
	* Individual: ObservationTarget consisting of one individual
	* Panel: ObservationTarget consisting of group of individuals
* Protocol: procedure of observation on a defined set of features
	* discussion: many-to-many OR xref relation with Feature?
	* see PhenotypeMethod discussion
* ProtocolApplication: one bundle of values for exactly one target
	* xref to ObservationTarget (e.g. Individual, but also SNP)
	* xref to Protocol
	* discussion: xref to DataSet?
* Observation: value relation between ProtocolApplication and ObservableFeature
	* xref to ProtocolApplication
	* xref to ObservableFeature
	* (no xref to Target, this is via ProtocolApplication)

'''organization'''
* Study: a bundle of experiments typically published in a paper
	* discussion: bundle of Experiment, i.e. StudyElement?
* Experiment: a story of experimental objectives and outcomes
	* discussion: refers to dataSets?
* DataSet: a group of ProtocolApplication
	* discussion: homogeneous (i.e. using one protocol only?)
* SelectionCriteria: conditions of relationship between Panel
	* xref to Source and Target panel
	* has: number of individuals, details
	* discussion: how to formalize

'''attribution'''
* Contact: an entity having contact details such as address
* Person: to refer to natural actors in the process
* Organization: organization actor
* PersonAffiliation: association between individual and Organization
* Submission: the event of data contribution
	* dicussion: what are Submissable items? I.e. can have Contribution
* Contribution: metadata describing Role of Person in a Study (?)

'''references'''
* Hotlinks: hyperlinks to external? Or internal?
* Citation: literature reference
	* discussion: what entities can have references?
* OntologyReference: reference to coding lists
	* Species: reference to species definitions
* AlternateIds: alternative identifiers
* FeatureAnnotion: qualitative association between Feature and OntologyTerm
	* has 'exactmatch' and 'description'
	
'''genome'''
* SequenceCharacteristic
	* Marker: genomic variable site
	* Allele: alternative alleles of marker
	* Genotype: valid genotypes for a marker
* SequenceRelation

	
'''gwas central specific'''
* FrequencyCluster
	* can be modelled as Protocol?
* GenotypeFrequency
	* can be modelled as Protocol?
* AlleleFrequency
	* can be modelled as Protocol?
* SamplePanel
	* is a Panel with panelType=SamplePanel?
	* is a Panel with panelType=AssayedPanel?
* UsedMarkerset
	* can be modelled as Protocol? or DataSet?
* EffectSize
	* can be modelled as Protocol?

== checklist of requirements ==

* study and person should have qualified 'contribution' denoting 'role' in study
* both study and data sets can be submissions (what else?)
* submission can have contributions (== role in submission)
* person can have more than one affiliation, how does that relate to role?
* remove fax and phone
* study design should come from an ontology
* need a way to link panels (e.g. sample panel, assayed panel)
* hotlinks to see only hotlinks related to a specific element, e.g only see experimental specific hotlinks in experiments?

== FAQ ==

Q: Where do I add panel specific information e.g. population information, number of males/females, Geographical location
>> A: these are a ProtocolApplication having panel as target
Q: where to add species?
>> A: species are special kind of ontology term