| | 1 | = OmicsConnect wiki = |
| | 2 | |
| | 3 | This page reports current issues and plans with omicsconnect, an extension on top of Observ. |
| | 4 | |
| | 5 | NB this document formatted in trac wiki format, so we can include it online. Syntax: |
| | 6 | * unsolved issues |
| | 7 | * ~~ solved issues ~~ |
| | 8 | >> comments |
| | 9 | |
| | 10 | == showstoppers == |
| | 11 | |
| | 12 | * mrefs master/detail forms don't behave well. Examples: |
| | 13 | * adding new citations for study. |
| | 14 | * adding new measurement to protocol |
| | 15 | |
| | 16 | == discussion items == |
| | 17 | |
| | 18 | * Phenotype method <-> protocol / measurement |
| | 19 | * Who does contribution: Person or an PersonAffiliation? |
| | 20 | |
| | 21 | == wanted entities == |
| | 22 | |
| | 23 | Domain model: |
| | 24 | |
| | 25 | '''observation''' |
| | 26 | * Characteristic: 'is a' or 'has a' statements about an object |
| | 27 | * ObservableFeature: characteristic observed (is/has) or question asked (what is?) |
| | 28 | * Measurement: feature defined by description, unit, dataType, permittedValue |
| | 29 | * PermittedValue: a categorical value state for Measurement |
| | 30 | * ObservationTarget: target of observation |
| | 31 | * Individual: ObservationTarget consisting of one individual |
| | 32 | * Panel: ObservationTarget consisting of group of individuals |
| | 33 | * Protocol: procedure of observation on a defined set of features |
| | 34 | * discussion: many-to-many OR xref relation with Feature? |
| | 35 | * see PhenotypeMethod discussion |
| | 36 | * ProtocolApplication: one bundle of values for exactly one target |
| | 37 | * xref to ObservationTarget (e.g. Individual, but also SNP) |
| | 38 | * xref to Protocol |
| | 39 | * discussion: xref to DataSet? |
| | 40 | * Observation: value relation between ProtocolApplication and ObservableFeature |
| | 41 | * xref to ProtocolApplication |
| | 42 | * xref to ObservableFeature |
| | 43 | * (no xref to Target, this is via ProtocolApplication) |
| | 44 | |
| | 45 | '''organization''' |
| | 46 | * Study: a bundle of experiments typically published in a paper |
| | 47 | * discussion: bundle of Experiment, i.e. StudyElement? |
| | 48 | * Experiment: a story of experimental objectives and outcomes |
| | 49 | * discussion: refers to dataSets? |
| | 50 | * DataSet: a group of ProtocolApplication |
| | 51 | * discussion: homogeneous (i.e. using one protocol only?) |
| | 52 | * SelectionCriteria: conditions of relationship between Panel |
| | 53 | * xref to Source and Target panel |
| | 54 | * has: number of individuals, details |
| | 55 | * discussion: how to formalize |
| | 56 | |
| | 57 | '''attribution''' |
| | 58 | * Contact: an entity having contact details such as address |
| | 59 | * Person: to refer to natural actors in the process |
| | 60 | * Organization: organization actor |
| | 61 | * PersonAffiliation: association between individual and Organization |
| | 62 | * Submission: the event of data contribution |
| | 63 | * dicussion: what are Submissable items? I.e. can have Contribution |
| | 64 | * Contribution: metadata describing Role of Person in a Study (?) |
| | 65 | |
| | 66 | '''references''' |
| | 67 | * Hotlinks: hyperlinks to external? Or internal? |
| | 68 | * Citation: literature reference |
| | 69 | * discussion: what entities can have references? |
| | 70 | * OntologyReference: reference to coding lists |
| | 71 | * Species: reference to species definitions |
| | 72 | * AlternateIds: alternative identifiers |
| | 73 | * FeatureAnnotion: qualitative association between Feature and OntologyTerm |
| | 74 | * has 'exactmatch' and 'description' |
| | 75 | |
| | 76 | '''genome''' |
| | 77 | * SequenceCharacteristic |
| | 78 | * Marker: genomic variable site |
| | 79 | * Allele: alternative alleles of marker |
| | 80 | * Genotype: valid genotypes for a marker |
| | 81 | * SequenceRelation |
| | 82 | |
| | 83 | |
| | 84 | '''gwas central specific''' |
| | 85 | * FrequencyCluster |
| | 86 | * can be modelled as Protocol? |
| | 87 | * GenotypeFrequency |
| | 88 | * can be modelled as Protocol? |
| | 89 | * AlleleFrequency |
| | 90 | * can be modelled as Protocol? |
| | 91 | * SamplePanel |
| | 92 | * is a Panel with panelType=SamplePanel? |
| | 93 | * is a Panel with panelType=AssayedPanel? |
| | 94 | * UsedMarkerset |
| | 95 | * can be modelled as Protocol? or DataSet? |
| | 96 | * EffectSize |
| | 97 | * can be modelled as Protocol? |
| | 98 | |
| | 99 | == checklist of requirements == |
| | 100 | |
| | 101 | * study and person should have qualified 'contribution' denoting 'role' in study |
| | 102 | * both study and data sets can be submissions (what else?) |
| | 103 | * submission can have contributions (== role in submission) |
| | 104 | * person can have more than one affiliation, how does that relate to role? |
| | 105 | * remove fax and phone |
| | 106 | * study design should come from an ontology |
| | 107 | * need a way to link panels (e.g. sample panel, assayed panel) |
| | 108 | * hotlinks to see only hotlinks related to a specific element, e.g only see experimental specific hotlinks in experiments? |
| | 109 | |
| | 110 | == FAQ == |
| | 111 | |
| | 112 | Q: Where do I add panel specific information e.g. population information, number of males/females, Geographical location |
| | 113 | >> A: these are a ProtocolApplication having panel as target |
| | 114 | Q: where to add species? |
| | 115 | >> A: species are special kind of ontology term |
