ASMS 2009
MSI supported by SetupX
Document Actions
How SetupX is supporting the Standardization in Metabolomics Experiments.
In order to make SetupX a repository that is full MSI compatible I created the following setup - this is first apporach:
Therefore each Attribute that was written down in the publications for MSI standards has to be defined in the System.
It requieres that each msi attribute has a unique label, definition, question, it supports a comment field and requires an extension for each attribute. In addition to that we keep track of who has defined this attribute as an MSI attribute and since when it exists.
TODO: add additional attribute if it is requiered or optional.
http://128.120.136.198:8080/m1/msi_attributes.jsp
http://128.120.136.198:8080/m1/msi_attributes_xml.jsp
it is actually a RSS feed so you can use it in your application or just in your news reader.
Or single Attributes:
http://128.120.136.198:8080/m1/msi_detail_attribute.jsp?id=156
http://128.120.136.198:8080/m1/msi_attribute_xml.jsp?id=156
http://128.120.136.198:8080/m1/curator.jsp
TODO - add attributes dropdown to sxSubmission frontend
Data unit - how is a date reported - proposed ISO8601FORMAT.
Another Problem - the curation needs to be support curation of data in "standard formats".
Define MSI Attributes
First step was that we needed a possibility to "techniclly" define HOW these Attributes look like.Therefore each Attribute that was written down in the publications for MSI standards has to be defined in the System.
It requieres that each msi attribute has a unique label, definition, question, it supports a comment field and requires an extension for each attribute. In addition to that we keep track of who has defined this attribute as an MSI attribute and since when it exists.
TODO: add additional attribute if it is requiered or optional.
Repository of MSI Attributes
Does it make sense to create a repository of MSI attributes just for ourself? - No. But we need to have a common list of attributes somewhere - so who ever wants to provide me another list of attributes electronicly - I would be happy to use it. Until then the list of MSI Attributes is publicly available as an XML file:http://128.120.136.198:8080/m1/msi_attributes.jsp
http://128.120.136.198:8080/m1/msi_attributes_xml.jsp
it is actually a RSS feed so you can use it in your application or just in your news reader.
Or single Attributes:
http://128.120.136.198:8080/m1/msi_detail_attribute.jsp?id=156
http://128.120.136.198:8080/m1/msi_attribute_xml.jsp?id=156
SX to MSI mapping
Now that we defined the MSI Attributes and they are electronicly available we can declare certain attributes stored in SetupX as MSI-Parametes - it is the process of matching the sxAttributes to msiAttributes. This is needed because the sxAttributes were defined earlier than the MSIattributes.http://128.120.136.198:8080/m1/curator.jsp
MSI in SetupX FrontEnd
How about MSI attributes that are not covered or that vary not only by experiment or by class but also by a single sample.TODO - add attributes dropdown to sxSubmission frontend
MSI Reporting
Now that we defined which of the Attributes is an actual MSI Attribute I can create MSI compatible Reports out of each of the experiments - as xml or with an overlying stylesheet also as an html report.Outlook
What happens to Attributes that are combined out of multiple Attributes. For example Harvest Date is Day and Time, Timepoints, Locations, ... This becomes obvious if you start to try to generate reports based on an SX experiment. The structure is simply missing.Data unit - how is a date reported - proposed ISO8601FORMAT.
Another Problem - the curation needs to be support curation of data in "standard formats".
Created by
zwluxx
Last modified 2007-10-19 12:59 PM
Last modified 2007-10-19 12:59 PM
