TODO (after PSI-MS meeting 25-26-27 June 2007) ==== Additional instance documents ----------------------------- - One that demonstrates the use of the acquisitionList and acquisition (essentially, one precursor scan, three MS/MS scans, that are then combined) - Make an example that shows a nice usage of CV in the 'sample' element (NEWT, Brenda, Cell Type Ontology, ...) - The existing examples have some changed CV terms. These need to be updated (after the identifiers for these terms have have been fixed). Validator ToDo's ---------------- - scan_numbers must be always increasing but need not be consecutive - spectrum ids must be unique within a file - scan numbers unique within run, identifiers unique within file - 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. Release schedule ---------------- July 1 limited circulation for comment August 1 Submission to Doc Proc September 1 Start of 60 day public review Oct 6 HUPO - When we send out the beta version of mzML for testing, send it to David Fenyo, Jayson, Randy, ISB, Patrick - We should get Rolf or someone to announce to whole assembly about mzML being in community review in Seoul (if indeed true) Web site -------- - Please post your notes. I don't need to review them, but can if you want. - I wonder if it makes sense and is easy to create a separate Lyon page and a separate EBI page so post notes and the state after those meetings, separate from the latest? - We should post the results on the web site soon. - Revise the links to point into CVS Items done ---------- - tiny1 in filecontent no SIM just MSn only - cvList count is wrong. should be 1 - Commit changes to tiny1 - I failed to get the psi-ms-dev and psi-ms-wg admin password. Luisa thought she knew it but didn't. Forgot to catch Chris Taylor who might know it. Can you ask around and dig it up? - would be useful to start making a text list of unusual validator rules - Check my CVS access Remaining list from Eric ------------------------ - Add mechanism to specify external sample LSID ref - never did make an acquisition list example - Consider the addition of nestedCvParam tag (with order?) - Can we come up with a reasonable example where this might be useful outside of sample? which probably shouldn't be extensive anyway - What about retention time? attribute or CvParam? - Anything else that should be an attribute instead of a cvParam? - Consider a way to annotate the min/max pH of a band for the run - Put together a document showing indexing - Email mzML state to Josh and ask him to update ReAdW & RAMP - index contains ?: spectrum_id="" run_id="" scan_number="" offset="" - Jimmy points out that mzXML encodes MRMs effectively like tiny MS2 scans with scanType=”MRM” - Let’s remember that the transition list will change over time within a run - Now that we’re allowing multiple runs in a file, how will the index look to handle this? - Matt Chambers asks for better definition of run 6/20 - Matt chambers asks about start/stop time, absolute time, order issues with dataProcessingList - Randy reminds that is important: mzML be stable and easy to support. Minimize “more than one way to do it”