Changes between Version 9 and Version 10 of Ticket #690, comment 30


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Timestamp:
Dec 9, 2014, 12:21:13 PM (9 years ago)
Author:
olle

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  • Ticket #690, comment 30

    v9 v10  
    11Background information update:
    22
    3  1. If input tube content is DNA/RNA:[[BR]]a. Either a single tube with DNA or RNA is delivered, or one tube with DNA and one tube with RNA.[[BR]]b. If RNA is delivered, the full amount is put in a freezer storage box.[[BR]]c. If DNA is delivered, some amount is used to create a DNA extract for further analysis. There ''might'' be a residue to put in a freezer storage box, but in the first version of !MeLuDi it is assumed that the full amount is used.
     3 1. If tube content is DNA/RNA:[[BR]]a. Either a single tube with DNA or RNA is delivered, or one tube with DNA and one tube with RNA.[[BR]]b. If RNA is delivered, the full amount is put in a freezer storage box.[[BR]]c. If DNA is delivered, some amount is used to create a DNA extract for further analysis. There ''might'' be a residue to put in a freezer storage box, but in the first version of !MeLuDi it is assumed that the full amount is used.
    44 2. If an FFPE (Formalin-Fixed, Paraffin-Embedded) tissue specimen is delivered, the number of sections (slices) should be stored with the specimen.
    55 3. Storage box name suffices should all be in lower-case, forcing the storage box suffix "`_Sp`" to be exchanged for "`_sp`".
    … …  
    77!Functional/Design specification update related to the background information update:
    88
    9  1. If input 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 an input 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 an input 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 input 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 `INPUT_TUBE_CONTENT_TYPE` ("`InputTubeContentType`") with options [`Specimen`, `DNA`, `RNA`, `DNA + RNA`] should be created and stored with the created case item.
    10  2. For FFPE input 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.
     9 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.
    1111 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`".
    1212
    1313Other design specification updates:
    1414
    15  1. Several annotations that are currently stored both for a case and its children specimen items, should be set for either case or specimens:[[BR]]a. Annotations of types `MUTATION_ANALYSIS` ("`MutationAnalysis`"), `PROJECT_FOCUS` ("`ProjectFocus`"), `SITE` ("`Site`"), and `INPUT_TUBE_CONTENT_TYPE` ("`InputTubeContentType`") should be stored with the case item.[[BR]]b. Annotations of types `SPECIMEN_TYPE` ("`SpecimenType`") and `NOF_SECTIONS` ("`NofSections`"), should be stored with specimen items.
     15 1. Several annotations that are currently stored both for a case and its children specimen items, should be set for either case or specimens:[[BR]]a. Annotations of types `MUTATION_ANALYSIS` ("`MutationAnalysis`"), `PROJECT_FOCUS` ("`ProjectFocus`"), `SITE` ("`Site`"), and `TUBE_CONTENT_TYPE` ("`TubeContentType`") should be stored with the case item.[[BR]]b. Annotations of types `SPECIMEN_TYPE` ("`SpecimenType`") and `NOF_SECTIONS` ("`NofSections`"), should be stored with specimen items.
    1616 2. Unused annotations and other items in current !MeLuDi version should be removed, in order to create a minimal release. This should be done even if the item in question with high probability will be needed in a future version (it will be included in that version instead).
    1717 3. Annotation type `SAMPLING_DATETIME` ("`SamplingDateTime`") of type `Type.TIMESTAMP` should be exchanged for annotation type `SAMPLING_DATE` ("`SamplingDate`") of type `Type.DATE`, since the sampling daytime is unknown in !MeLuDi.