Changes between Version 11 and Version 12 of Ticket #690, comment 30


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Timestamp:
Dec 11, 2014, 11:23:01 AM (8 years ago)
Author:
olle
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  • Ticket #690, comment 30

    v11 v12  
    88
    99 1. If tube content is DNA or RNA:[[BR]]a. Instead of a specimen item, a DNA extract or RNA extract item should be created.[[BR]]b. A DNA extract item from a tube should have a name consisting of the case name followed by "`.d`", e.g. for case "`ML00001`" the DNA extract name will be "`ML00001.d`".[[BR]]c. An RNA extract item from a tube should have a name consisting of the case name followed by "`.r`", e.g. for case "`ML00001`" the RNA extract name will be "`ML00001.r`".[[BR]]d. Currently annotation `SAMPLE_TYPE` ("`SampleType`") with possible value [`unknown`, `Primary tumour`, `Metastasis`, `DNA`, `RNA`] is used to indicate the content of a specimen tube, and is stored both for the created case and child items. There are several problems with this; one is that the two options `Primary tumour` and `Metastasis` are intended for FFPE specimen items, another is that the name "`SampleType`" is inappropriate for DNA and RNA items, that are of type `Extract`, instead of `Sample`. Options [`unknown`, `Primary tumour`, `Metastasis`] should be stored in annotation of type `SPECIMEN_TYPE` ("`SpecimenType`") for specimen items, while a new annotation type `TUBE_CONTENT_TYPE` ("`TubeContentType`") with options [`Specimen`, `DNA`, `RNA`, `DNA + RNA`] should be created and stored with the created case item.
    10  2. For FFPE tube content:[[BR]]a.Annotationtype `NOF_PIECES` ("`NofPieces`"), used for tissue specimens, should be exchanged for new annotation type `NOF_SECTIONS` ("`NofSections`"), which is more appropriate for FFPE specimens.[[BR]]b. When registering an FFPE sample, an input field for the number of sections should be added (default should be "`1`"). The value should be stored in the new `NOF_SECTIONS` ("`NofSections`") annotation type for the created specimen item.
    11  3. Java servlet class/file `SpecimenTubeServlet.java` in `src/net/sf/basedb/meludi/servlet/` should be updated in storage box queries to search for names ending with "`_sp`", instead of "`_Sp`".
     10 2. For FFPE tube content:[[BR]]a. Annotationtype `NOF_PIECES` ("`NofPieces`"), used for tissue specimens, should be exchanged for new annotation type `NOF_SECTIONS` ("`NofSections`"), which is more appropriate for FFPE specimens.[[BR]]b. When registering an FFPE sample, an input field for the number of sections should be added (default should be "`1`"). The value should be stored in the new `NOF_SECTIONS` ("`NofSections`") annotation type for the created specimen item.
     11 3. For DNA and/or RNA tube content:[[BR]]a. Until more information exists regarding what data is supplied with incoming DNA and RNA tubes, only the name, creation date, and extraction date ("Sampling date" input field) will be stored with these items. Specifically, this means that no PL-number or PAD/CL-number will be stored for a case having no specimens.
     12 4. Java servlet class/file `SpecimenTubeServlet.java` in `src/net/sf/basedb/meludi/servlet/` should be updated in storage box queries to search for names ending with "`_sp`", instead of "`_Sp`".
    1213
    1314Other design specification updates: