Changes between Version 2 and Version 3 of ObservMeetings/2012_04_03
- Timestamp:
- 2012-04-11T12:44:03+02:00 (13 years ago)
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ObservMeetings/2012_04_03
v2 v3 3 3 Att: Rob, Joeri, Morris 4 4 5 During the meeting the first prototype and experiences loading data were discussed. This resulted in a long list of issues: 5 During this meeting the first prototype and experiences loading data were discussed. 6 (source: molgenis_apps/build_omicsconnect.xml) 6 7 7 * Attach existing mrefs via subform 8 >>now, if you have an mref from parent->subform and you [add new] the new entity is not shown because the mref is parentform is not updated 9 * mref nulls are not checked 10 * DataSource on chromosome is used to define what genome build the chromosome is in. 11 * HotLink mechanism needs more work (parked for now) 12 * We want example data sets for: 13 * gwas (SNV, CNV) 14 * pheno 15 * exome (Rob has example paper for that) 16 * protocols 17 * We urgently need a TableView 18 * A new module therefore will be created by Joris (other project) 19 * StudyAnalysis 8 This resulted in a long list of issues: 20 9 21 == part 1==10 == References == 22 11 * Accession and accession version is confusing 23 12 * Proposed solution: use OntologyTerm table (or similar) to manage all accessions centrally. 24 13 * PrimaryCitation -> update label to use not id but something more meaningful (what exactly? pubmedid? nice would be 'Adamusiak et al (2011) Human Mutation) 14 * Accession 15 * Many items should have accessions / alternateIds + versions 16 * Proposal: central Accession table analogous to OntologyTerm (we could actually used OntologyTerm????) 17 18 == Panel == 25 19 * Panel.name -> Panel.identifier 26 20 * remove Panel.ontologyReference 27 * We would really like a way to create more filtered OntologyReferences. Ideally these would be like 'saved filters' as users may have multiple ways to choose their ontology terms.28 21 * Add user interface to add 'species' 29 22 * We need to link Panel -> other Panel (as subform of Panel) to being able to assemble panels from other panels using some SelectionCriteria 23 24 == Study organization == 30 25 * link Contributions <-> Study is missing (as consequence all contributions are shown) 31 26 * Need more types of contribution types/roles … … 33 28 * multiple affiliations 34 29 * Action: 35 == part 2 ==36 30 * StudyAnalysisMethod = "protocols during study" or "used protocols" 37 31 * todo: remove OntologyReference … … 39 33 * Field 'name' should become 'identifier' (unique) 40 34 * optionally data model can have human readible names 35 * Citation.publicationStatus should be xref->OntologyTerm 36 * Experiment.design should be xref->OntologyTerm 37 * DataSet.protocolParameters 38 * Discussion: proposal to remove and instead refer to the Protocol (that has parameters) 39 40 == Protocols and Measurement == 41 * Do we really need Measurement? Can we not just use ObservableFeature directly? 41 42 * Measurement gets lost when adding to subform of Protocol 42 43 * this is the mref issue mentioned above … … 44 45 * Study uses Protocol (multiple studies may) 45 46 * Protocol uses Measurement (so indirectly the link is there) 46 * Citation.publicationStatus should be xref->OntologyTerm47 * Experiment.design should be xref->OntologyTerm48 * DataSet.protocolParameters49 * Discussion: proposal to remove and instead refer to the Protocol (that has parameters)50 47 * Protocol.features -> rename to Protocol.parameters as it is confusing 51 48 * Protocol.circumstances -> unclear, remove (people can use parameters instead?) … … 56 53 * Discussion: lookup label is now (Study_name:Experiment_name) 57 54 58 == part 3==55 == GWAS specific == 59 56 * Significances + Frequencies 60 57 * Change superclass (these are NOT ProtocolApplication) … … 71 68 * add 'autosomal' 72 69 * add 'order number' 73 * Accession74 * Many items should have accessions / alternateIds + versions75 * Proposal: central Accession table analogous to OntologyTerm (we could actually used OntologyTerm????)76 70 * Marker 77 71 * remove 'label' … … 86 80 * what is 'target' (confusing because we use it in other meaning) 87 81 88 89 Actions: 82 == Actions == 90 83 * Joeri will add xQTL extensions to OmicsConnnect 91 84 * Morris will add NGS (Genome of NL) extensions to OmicsConnect 92 85 * Morris will process as far as he can todos from this meeting in the model 93 86 * Rob will integrate citation lookup (of gwascentral curation tool) to OmicsConnect 94 * Later discuss contribution model with Mummy, in particular issue on how to deal with affiliations/roles 87 * Later: discuss contribution model with Mummy, in particular issue on how to deal with affiliations/roles 88 * All: create / get example data!
