Ticket #1153: sequencing-draft-2.txt

File sequencing-draft-2.txt, 4.9 KB (added by Nicklas Nordborg, 13 years ago)
1Summary of changes and additions for supporting sequencing
41. Remove [LabeledExtract] and [Label]. Existing labeled
5 extracts are converted to [Extract] items with a subtype.
6 Existing labels are converted to [Tag] items with a subtype.
7 We define two subtypes for tags ('Label' and 'Barcode'),
8 and two subtypes for extracts ('LabeledExtract' and 'Library').
9 Extracts can be tagged with a [Tag].
12 What about protocol types? What do we do with the current
13 LABELING protocol type? It would be useful to define more
14 protocol types, for example, 'Library preparation'. But
15 how do we know which protocol type is the correct one?
16 Can we add a link between [ItemSubtype] and [ProtcolType]
17 which means that when an item of the given subtype is
18 created the protocol should be from the linked protocol
19 type?
22 Do we need some kind of 'mode' setting in the GUI so that it uses
23 the correct terminology as much as possible? The 'mode' setting
24 could also control parts of the 'Validate' functionality in the
25 'Item overview' which may need to work differently. Particularly
26 all rules for 'number of channels' which are only needed for microarray
27 experiments.
302. Changes in [BioMaterialEvent]
32 A new entity class [BioMaterialParent] is introduced instead of
33 the "anonymous" link-table 'BioMaterialEventSources'.
34 This should make it possible to get rid of the [UsedQuantity]
35 "fulhack" that was used to support multi-array slides.
36 Existing information can easily be moved to the new tables.
38 The parent and pooled properties are modified so that the
39 parent may hold a SINGLE biomaterial of the same type or
40 of the parent type. The pooled flag should only be used when
41 there are two or more parents (of the same type).
43 The 'Hybridization' event type is changed to 'BioAssayCreation'.
44 The link between [BioMaterialEvent] and [Hybridization] is replaced
45 with a link to [PhysicalBioAssay].
473. New entity class [PhysicalBioAssay] that replaces [Hybridization]
49 Existing hybridizations are converted to [PhysicalBioAssay] items
50 with a subtype. We define two subtypes: 'Hybridization' and '???'.
52 The [PhysicalBioAssay] should implement [FileStoreEnabled] so
53 that we can link files to it.
55 New [ProtocolType]: 'Sequencing'
56 New [HardwareType]: 'Sequencing station'
57 New [Hardware]: 'HiSeq 2000'
59 See also discussion above about protocol types and item subtypes.
614. Changes for [FileSet] and related classes
63 [FileSetMember] is made into an [Annotatable] item so that
64 we can add annotations on files.
66 [FileSet] is modified so that it becomes possible to add more
67 than one file for each [DataFileType]. But this is controlled
68 by a flag ('allowMultiple').
70 See ticket #1604 for more information about this.
725. New entity classes [BioAssayEvent], [DerivedBioAssaySet] and
73 [DerivedBioAssay] that replaces [Scan] and [Image]
75 The [BioAssayEvent] and [DerivedBioAssaySet] makes up a loop
76 that is started from a [PhysicalBioAssay] and ends with a
77 [RawBioAssay]. This loop is similar to the loop with [Transformation]
78 and [BioAssaySet] in the existing analysis section.
80 Existing [Scan] and [Image] data is moved into a single "iteration"
81 of that loop. The scan data is split between the bioassay event
82 (protocol, scanner, date) and the derived bioassay set
83 (name, description, owner). One or more derived bioassays are also
84 created with links back to the biomaterial they are related to.
85 Image data is moved to the file set of the derived bioassay set
86 with the properties (jpeg, tiff, etc.) added as annotations.
88 The new classes can be used to represent the multiple steps
89 that are required before sequenced data can be boiled down to
90 something that is similar to expression data.
92 A bioassay event can be linked with [Job], [Protocol],
93 [Hardware] and [Software]. It should be possible to
94 create iterations both manually and with plug-ins.
96 The existing 'Analysis' [PluginType] is re-used. Since plug-ins are
97 required to implement context-checking there shouldn't be any risk
98 of mixing things up.
100 For gui things we probably need a new plug-in similar to the
101 'Manual transform' plug-in that exists for the experiment analysis
102 section. Maybe we can provide configurations for some of the
103 software mentioned below.
105 New [Software]: BCL Converter, Casava, Bowtie, Myrna, Tophat,
106 Cufflinks, and more???
108 New [DataFileType]: bcl, cif, fastq, qseq, bam, sam, and more???
109 Which ones do we really want to store/reference through BASE?
111 New [FileType]: ????
113 New [Platform]/[PlatformVariant]: ???
115 Or should most of this be in an extensions package similar to
116 the existing Illumina package?