| 1 | | = OmicsConnect wiki = |
| 2 | | |
| 3 | | This page reports current issues and plans with omicsconnect, an extension on top of Observ. |
| 4 | | This work is in the context of EU-BioSHARE WP4. |
| 5 | | |
| 6 | | NB this document formatted in trac wiki format, so we can include it online. Syntax: |
| 7 | | * unsolved issues |
| 8 | | * ~~ solved issues ~~ |
| 9 | | >> comments |
| 10 | | |
| 11 | | == showstoppers == |
| 12 | | |
| 13 | | * mrefs master/detail forms don't behave well. Examples: |
| 14 | | * adding new citations for study. |
| 15 | | * adding new measurement to protocol |
| 16 | | |
| 17 | | == discussion items == |
| 18 | | |
| 19 | | * Phenotype method <-> protocol / measurement |
| 20 | | * Who does contribution: Person or an PersonAffiliation? |
| 21 | | |
| 22 | | == WormQTL datatypes review == |
| 23 | | '''v1 -> v2: notes''' |
| 24 | | * analysis -> computeprotocol: needs merging work |
| 25 | | * derivedtrait -> MISSING: observablefeature is what you want, but this needs to be typed in some way |
| 26 | | * parameterset -> mref 'parameters' in computeprotocol: look into consequences not having sets for this |
| 27 | | * binarydatamatrix -> MISSING: matrix backend specific, link to binary storage files |
| 28 | | * gene -> MISSING: probably sequencecharacteristic? how is this typed? must be subclassed first? fields such as xref to Chromosome, bp location, etc via sequencerelation? |
| 29 | | * parametervalue -> computeparameter: better than before with datatyping/freerange values |
| 30 | | * chromosome -> chromosome: missing some handy fields such as 'orderNr' and 'isAutosomal' ('rank' in sequencerelation?) |
| 31 | | * investigation -> study: OK |
| 32 | | * probe -> [see: gene] |
| 33 | | * data -> dataset: might need some extra fields such as ValueType, ColumnType, RowType, Storage, etc |
| 34 | | * marker -> marker: missing some fields: xref to Chromosome, cM location, reportsFor. 'seqlength' as int might be too small? (2x10^9 when signed) |
| 35 | | * runtimeproperty -> MISSING: but make molgenis-wide build-in? |
| 36 | | * dataname -> computeparameter: if values can be proper XREFs |
| 37 | | * measurement -> [see: derivedtrait] |
| 38 | | * sample -> MISSING: subclass of observationtarget? |
| 39 | | * dataset -> [see: parameterset, if values can be proper XREFs] |
| 40 | | * panel -> panel: OK |
| 41 | | * snp -> [see: gene] |
| 42 | | * datavalue -> computeparameter: if values can be proper XREFs |
| 43 | | * parametername -> computeparameter: OK |
| 44 | | * transcript -> [see: gene] |
| 45 | | * investigationfile -> MISSING: but debatable use/implementation |
| 46 | | |
| 125 | | == checklist of requirements == |
| 126 | | |
| 127 | | * study and person should have qualified 'contribution' denoting 'role' in study |
| 128 | | * both study and data sets can be submissions (what else?) |
| 129 | | * submission can have contributions (== role in submission) |
| 130 | | * person can have more than one affiliation, how does that relate to role? |
| 131 | | * remove fax and phone |
| 132 | | * study design should come from an ontology |
| 133 | | * need a way to link panels (e.g. sample panel, assayed panel) |
| 134 | | * hotlinks to see only hotlinks related to a specific element, e.g only see experimental specific hotlinks in experiments? |
| 135 | | |
| 136 | | == FAQ == |
| 137 | | |
| 138 | | Q: Where do I add panel specific information e.g. population information, number of males/females, Geographical location |
| 139 | | >> A: these are a ProtocolApplication having panel as target |
| 140 | | Q: where to add species? |
| 141 | | >> A: species are special kind of ontology term |
