| | 1 | == Minutes OmicsConnect 2012_04_03 == |
| | 2 | |
| | 3 | Att: Rob, Joeri, Morris |
| | 4 | |
| | 5 | During the meeting the first prototype and experiences loading data were discussed. This resulted in a long list of issues: |
| | 6 | |
| | 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 |
| | 20 | |
| | 21 | == part 1 == |
| | 22 | * Accession and accession version is confusing |
| | 23 | * Proposed solution: use OntologyTerm table (or similar) to manage all accessions centrally. |
| | 24 | * PrimaryCitation -> update label to use not id but something more meaningful (what exactly? pubmedid? nice would be 'Adamusiak et al (2011) Human Mutation) |
| | 25 | * Panel.name -> Panel.identifier |
| | 26 | * 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 | * Add user interface to add 'species' |
| | 29 | * We need to link Panel -> other Panel (as subform of Panel) to being able to assemble panels from other panels using some SelectionCriteria |
| | 30 | * link Contributions <-> Study is missing (as consequence all contributions are shown) |
| | 31 | * Need more types of contribution types/roles |
| | 32 | * multiple roles (author, design, grant holder) |
| | 33 | * multiple affiliations |
| | 34 | * Action: |
| | 35 | == part 2 == |
| | 36 | * StudyAnalysisMethod = "protocols during study" or "used protocols" |
| | 37 | * todo: remove OntologyReference |
| | 38 | * todo: create better protocol editor (mref is confusing) |
| | 39 | * Field 'name' should become 'identifier' (unique) |
| | 40 | * optionally data model can have human readible names |
| | 41 | * Measurement gets lost when adding to subform of Protocol |
| | 42 | * this is the mref issue mentioned above |
| | 43 | * Measurement should not have direct xref to study, because |
| | 44 | * Study uses Protocol (multiple studies may) |
| | 45 | * Protocol uses Measurement (so indirectly the link is there) |
| | 46 | * Citation.publicationStatus should be xref->OntologyTerm |
| | 47 | * Experiment.design should be xref->OntologyTerm |
| | 48 | * DataSet.protocolParameters |
| | 49 | * Discussion: proposal to remove and instead refer to the Protocol (that has parameters) |
| | 50 | * Protocol.features -> rename to Protocol.parameters as it is confusing |
| | 51 | * Protocol.circumstances -> unclear, remove (people can use parameters instead?) |
| | 52 | * Hotlink |
| | 53 | * Still unclear on how to generalize; for now just apply to Study |
| | 54 | * UsedMarkerset |
| | 55 | * remove link to Study (because already links to Experiment) |
| | 56 | * Discussion: lookup label is now (Study_name:Experiment_name) |
| | 57 | |
| | 58 | == part 3 == |
| | 59 | * Significances + Frequencies |
| | 60 | * Change superclass (these are NOT ProtocolApplication) |
| | 61 | * Discussion if we can remove and instead use DataSet |
| | 62 | * Are these part of a DataSet i.e. a particular kind of data set? |
| | 63 | * Changer marker to be xref (instead of text) |
| | 64 | * remove odds ration and attr risk |
| | 65 | * PhenotypeProperty (is confusing compared to Measurement) |
| | 66 | * Property = Measurement? |
| | 67 | * Method = Protocol |
| | 68 | * More discussion needed? Would be nice to merge PhenotypeProperty with Measurement. |
| | 69 | * Chromosome |
| | 70 | * remove xref to study |
| | 71 | * add 'autosomal' |
| | 72 | * add 'order number' |
| | 73 | * Accession |
| | 74 | * Many items should have accessions / alternateIds + versions |
| | 75 | * Proposal: central Accession table analogous to OntologyTerm (we could actually used OntologyTerm????) |
| | 76 | * Marker |
| | 77 | * remove 'label' |
| | 78 | * add c.dna and pdna notation? |
| | 79 | * residues and alleleSequence are same thing (remove alleleSequence) |
| | 80 | * validationCode should be xref->OntologyTerm |
| | 81 | * remove 'added from source build' |
| | 82 | * should alleles be stored elsewhere (see Allele table)? |
| | 83 | * PermittedGenotypes |
| | 84 | * residue-info |
| | 85 | * what is 'locgroup' (chado heritance) |
| | 86 | * what is 'target' (confusing because we use it in other meaning) |
| | 87 | |
| | 88 | |
| | 89 | Actions: |
| | 90 | * Joeri will add xQTL extensions to OmicsConnnect |
| | 91 | * Morris will add NGS (Genome of NL) extensions to OmicsConnect |
| | 92 | * Morris will process as far as he can todos from this meeting in the model |
| | 93 | * 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 |
