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h1. |
Question:
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How
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do
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I
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add
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an
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organism
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to
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the
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Organism
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List
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in
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caArray?
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Topic
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:
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caArray
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Usage
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Release
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:
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Up
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to
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caArray
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2.2
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Date
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entered
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:
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03/06/2009
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Details
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about
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the
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Question
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I
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did
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not
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see
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my
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sample
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organism
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on
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the
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Organism
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list.
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How
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can
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I
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add
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mine
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to
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the
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list?
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Answer
Organism List
"Organism"
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represents
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the
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source
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of
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sample
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biomaterial
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used
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in
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an
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experiment.
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It
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is
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one
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of
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the
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mandatory
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fields
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describing
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each
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caArray
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experiment.
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An
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initialization
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script,
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which
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is
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part
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of
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the
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caArray
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installation
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package,
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will
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insert
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the
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most
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commonly
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used
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organisms
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into
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caArray's
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database
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table:
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Organism
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.
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The
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organisms
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can
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then
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be
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selected
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from
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two
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drop-down
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lists
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in
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following
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sections:
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- Create
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- New
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- Experiment
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- Import
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- New
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- Array
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- Design
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Manually
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Adding
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Organism
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If
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the
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organism
...
list
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in
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caArray
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does
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not
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contain
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the
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organism
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for
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your
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samples,
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there
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are
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two
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other
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ways
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to
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add
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new
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organisms
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into
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caArray.
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- Any
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- new
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- organism
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- defined
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- in
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- the
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- MAGE-TAB
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- Annotation
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- files
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- (
...
...
...
...
...
...
...
...
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- )
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- that
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- are
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- used
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- to
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- annotate
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- experiments
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- will
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- be
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- automatically
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- added
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- to
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- caArray's
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- database
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- during
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- the
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- data
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- file
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- import.
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- The
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- organism
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- is
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- defined
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- in
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- MAGE-TAB's
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- SDRF
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- file
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- following
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- the
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- sample
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- source
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- definition.
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- It
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- has
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- the
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- column
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- heading
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- "Characteristics
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- [MATKC:Organism
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- ].
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- New
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- organisms
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- can
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- also
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- be
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- manually
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- added
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- at
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- the
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- database
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- level.
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- The
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- SQL
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- statement
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- below
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- is
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- a
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- simple
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- insert
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- statement
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- that
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- can
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- be
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- used
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- to
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- add
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- a
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- new
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- entry
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- to
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- Organism
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- table:
| Code Block |
|---|
{code} insert into organism (ncbi_taxonomy_id, common_name, scientific_name, taxonomy_rank, term_source) select 9606, 'human', 'Homo sapiens', 'species', id from term_source where term_source.name='ncbitax'; {code} |
There
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are
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two
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fields
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that
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need
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to
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be
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clarified
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in
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this
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SQL
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statement:
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- term_source:
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- This
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- is
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- a
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- numeric
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- field.
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- It
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- is
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- really
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- the
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- term
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- source
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- identifier,
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- ID,
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- from
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- term_source
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- table.
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- In
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- the
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- example
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- above,
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- the
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- scientific
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- name
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- is
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- defined
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- in
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- the
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...
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- ,
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- a
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- known
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- source
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- already
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- defined
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- in
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- the
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- term_source
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- table.
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- If
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- your
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- taxonomy
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- source
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- is
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- not
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- in
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- the
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- Term_Source
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- table
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- yet,
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- it
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- needs
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- to
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- be
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- added
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- into
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- the
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- Term_Source
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- table
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- prior
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- to
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- executing
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- this
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- insert
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- statement.
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- ncbi_taxonomy_id:
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- it
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- is
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- the
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- taxonomy
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- ID
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- used
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- by
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- ncbitax.
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Prior
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to
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any
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database
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modification,
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a
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database
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backup
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is
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highly
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recommended.
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Have
...
a
...
comment?
...
Please
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leave
...
your
...
comment
...
in
...
the
...
...
...
| Wiki Markup |
|---|
Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=577].
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