Wednesday, 27 June 2007 ======================= Present: - Eric Deutsch - Jim Schofstahl - Puneet Souda - Luisa Montecchi-Palazzi - Lennart Martens 'Tiny1' example update ---------------------- - Eric: updating tiny1 to conform to the latest changes. Schema changes -------------- - Luisa: changed all complex type names by affixing 'Type' - Luisa: spotted a weird mzML element nested complexType. Resolved this by 'flattening it out' over the element. - Luisa: another problem is the current definition of the 'binary' part in 'spectrum', which has to be base64 binary data; this gives problems when entering 32-bit data in there. - Lennart: recreated a revised version of the abstract ComponentType, and made source, analyzer and detector instances of that abstract type. The ComponentType now also has a mandatory 'order' attribute. - Lennart: also introduced a ComponentList to hold the components (this update corresponds to a modified solution 2 as annotated Tuesday - it uses the inheritance, but retains the top-level element tags) - Luisa: sent revised schema to Samuel Kerrien to attempt JAXB code generation on it. - Luisa: should we have a TaxID attribute on sample? - Eric, Lennart: what about unknown samples, sample mixtures, chimaeric samples, non-life sciences (synthetic) samples? - Luisa: you can have 'undefined' or 'synthetic molecule'? - Lennart: but it still is too life-sciences centric. - All: let's go through the elements, see which we will require or not. - Lennart: Revised ParamGroup; 'id' is now removed, and a subclass 'ReferenceableParamGroup' is created that adds this 'id'. The 'ParamGroupList' at the top (for inlining collections of CV params) now is 'ReferenceableParamGroupList' and is the only place where 'ReferenceableParamGroup' is allowed. So only one place can store paramgroups that can be referenced, everywhere else is stuff that can only reference these. - Luisa, Lennart, Eric: Recursion of 'cvParam' within 'cvParam' is removed. If ever necessary again, Lennart will put it back in, in such a way htat only one level of recursion is possible. - All: attributes: + mzML element: 'id' should be required, and for lack of better a thing, should at least be the mzML filename at time of writing. + All 'count' attributes on lists will become required. - All: changed several names to make 'ABCType' consistent with element 'aBC'. - 'admin' section renamed to 'fileDescription'. - Added 'source' prefix to all 'SourceFileType' attributes CV changes ---------- - Luisa: we should change the filename, because it currently looks like na ontology, and we should call it something with CV. - Eric: all terms are capitalized in the CV. Should we not have only capitalization where proper names are used? - Luisa: agreed. - Luisa: the namespace should be changed from 'PSI'to 'PSI-MS' (abbreviation on OBO: 'MS'). - Luisa: should we have a mapping file or keep the old 'PSI' identifiers as 'secondary' identifiers? - Lennart: since the old CV wasn't very good, I would prefer mapping file only, and deprecating the old identifiers without further assignment as 'secondary'. - Eric: SourceFileType has an attribute 'fileType' which should come from the CV. - 'Attribute' and 'Action' are split ('action' is boolean, 'attribute' is numerical value) Validator --------- - Instrument should have at least one 'model' cvParam. This has to be validated by the validator as it is really hard to do on the schema. - SourceFileType has an attribute 'fileType' which should be verified against the CV. - 'BinaryArrayDataType', attributes 'dataType' and 'compressionType' should come from the CV. - 'Acquisition' - 'methodOfCombination' should come from the CV. - Split between 'Attribute' and 'Action' changes the way attribute validation should be done. Planning for submission & next days ----------------------------------- - Transorm existing instance documents - Trivial documents for complicated instruments - Acquisition instance document - Index needs doing - SpecDoc needs to be done - CV/schema mapping document (for validator) - Validator? - Update website + minutes + documents + pictures