added its annotation, and also new data standard split

SIBarcodeNetwork · Feb 17, 2016 · d5c583f · d5c583f
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diff --git a/Docs/barcode_data_standard.rst b/Docs/barcode_data_standard.rst
@@ -0,0 +1,64 @@
+Barcode Data Standard
+=====================
+
++----------------------------------------+---------------------+------------------------------+
+| **Specimen Metadata**                                                                       |
++========================================+=====================+==============================+
+| | **Text from Standard**               | **GenBank Field**   | **Required or Recommended?** |
++----------------------------------------+---------------------+------------------------------+
+| | "a unique identifier for the voucher | specimen_voucher    | Required                     |
+| | specimen using a structured field    |                     |                              |
+| | specified by CBOL and NCBI"          |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "the name of a formally described    | organism            | Required                     |
+| | species or a provisional label for   |                     |                              |
+| | an unpublished species"              |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "Country-Code using the controlled   | country             | Required                     |
+| | vocabulary used by GenBank"          |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "Latitude and longitude"             | lat_lon             | Strongly recommended         |
++----------------------------------------+---------------------+------------------------------+
+| | "Name of the identifier"             | identified_by       | Strongly recommended         |
++----------------------------------------+---------------------+------------------------------+
+| | "Name of the collector"              | collected_by        | Strongly recommended         |
++----------------------------------------+---------------------+------------------------------+
+| | "Date of collection"                 | collection_date     | Strongly recommended         |
++----------------------------------------+---------------------+------------------------------+
+| **Sequence Metadata**                                                                       |
++----------------------------------------+---------------------+------------------------------+
+| | **Text from Standard**               | **GenBank Field**   | **Required or Recommended?** |
++----------------------------------------+---------------------+------------------------------+
+| | "Come from a gene region             | gene                | Required                     |
+| | accepted by CBOL as an effective     |                     |                              |
+| | barcode" ... "Include the name of    |                     |                              |
+| | the region used"                     |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "the sequences of all forward and    | PCR_primers         | Required                     |
+| | reverse primers used"                |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "the names of the forward and        | PCR_primers         | Strongly recommended         |
+| | reverse primers"                     |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "trace files for the forward and     | NCBI Trace Archive  | Required                     |
+| | reverse sequencing runs              |                     |                              |
+| | submitted to the NCBI Trace          |                     |                              |
+| | Archive or the Ensembl Trace         |                     |                              |
+| | Server"                              |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+| | "at least 75% contiguous, high       | nucleotide_sequence | Required                     |
+| | quality bases from within the        |                     |                              |
+| | approved barcode region"             |                     |                              |
++----------------------------------------+---------------------+------------------------------+
+
+Specimen Metadata
+-----------------
+
+Collection Metadata
+~~~~~~~~~~~~~~~~~~~
+
+Voucher Metadata
+~~~~~~~~~~~~~~~~
+
+Sequence Metadata
+-----------------
diff --git a/Docs/bwp_data_standard.rst b/Docs/bwp_data_standard.rst
@@ -0,0 +1,3 @@
+BWP Data Standard Extension
+===========================
+
diff --git a/Docs/data_standard.rst b/Docs/data_standard.rst
diff --git a/Docs/images/add_annotation_button.png b/Docs/images/add_annotation_button.png
diff --git a/Docs/images/add_annotation_window.png b/Docs/images/add_annotation_window.png
diff --git a/Docs/images/annotating_consensus.png b/Docs/images/annotating_consensus.png
diff --git a/Docs/images/annotation_add_property.png b/Docs/images/annotation_add_property.png
diff --git a/Docs/images/annotation_after_drag.png b/Docs/images/annotation_after_drag.png
diff --git a/Docs/images/annotation_before_drag.png b/Docs/images/annotation_before_drag.png
diff --git a/Docs/images/annotation_interval.png b/Docs/images/annotation_interval.png
diff --git a/Docs/index.rst b/Docs/index.rst
@@ -3,7 +3,8 @@ Welcome to the Barcode of Wildlife Project Informatics documentation!
 
 * **Background and Getting Started**
 	* :doc:`setup_software`
-	* :doc:`data_standard`
+	* :doc:`barcode_data_standard`
+	* :doc:`bwp_data_standard`
 	* :doc:`conventions`
 * **Field Information Management System (FIMS)**
 	* :doc:`fims_spreadsheet_pop`
@@ -19,6 +20,7 @@ Welcome to the Barcode of Wildlife Project Informatics documentation!
 	* :doc:`sequence_qc`
 	* :doc:`mark_pass`
 	* :doc:`gb_upload`
+	* :doc:`its_annotation`
 
 Full Index
 ----------
@@ -27,7 +29,8 @@ Full Index
 	:maxdepth: 2
 
 	setup_software
-	data_standard
+	barcode_data_standard
+	bwp_data_standard
 	conventions
 	fims_spreadsheet_pop
 	fims_spreadsheet_val
@@ -39,4 +42,5 @@ Full Index
 	assembling_contigs
 	sequence_qc
 	mark_pass
-	gb_upload
+	gb_upload
+	its_annotation
diff --git a/Docs/its_annotation.rst b/Docs/its_annotation.rst
@@ -0,0 +1,75 @@
+Annotating for ITS GenBank Upload
+=================================
+
+Since ITS1 and ITS2 are not genes and do not encode proteins, you cannot use the automated "Add Gene & CDS features" button. You are going to have to individually annotate each sequence.
+
+Here are a couple of example ITS records that show what we will be trying to achieve: http://www.ncbi.nlm.nih.gov/nuccore/JN253283
+and http://www.ncbi.nlm.nih.gov/nuccore/KT960182
+
+Adding the Annotation
+---------------------
+
+To annotate an assembly, make sure you are on the Contig View tab, and click select the consensus sequence by clicking the Consensus label.
+
+.. figure:: /images/annotating_consensus.png
+  :align: center
+  :target: /en/latest/_images/annotating_consensus.png
+
+Once the consensus sequence is selected, click the "Add/Edit Annotation" button.
+
+.. figure:: /images/add_annotation_button.png
+  :align: center
+  :target: /en/latest/_images/add_annotation_button.png
+
+This will bring up the "Add annotation" window.
+In the Name box, enter any name that describes this annotation. For this example, I named it "ITS2 Annotation". For Type, select "Misc_RNA". Then make sure that Track is "No Track", and select "Undirected" for Direction.
+
+In the Properties section, click the Add button to bring up the "Add Property" window.
+For "Name", enter "product", and for "Value" enter "internal transcribed spacer 2". Click OK.
+
+.. figure:: /images/annotation_add_property.png
+  :align: center
+  :target: /en/latest/_images/annotation_add_property.png
+
+Finally, in the Intervals section, select the number range that is already there, and click "Edit". Make sure that both the "Truncated left end" and "Truncated right end" options are selected. Click OK.
+
+Your completed window should now look like this:
+
+.. figure:: /images/add_annotation_window.png
+  :align: center
+  :target: /en/latest/_images/add_annotation_window.png
+
+Click OK, and the ITS2 annotation will be added to the consensus portion of the assembly.
+
+.. figure:: /images/annotating_consensus.png
+  :align: center
+  :target: /en/latest/_images/annotating_consensus.png
+
+The annotation has been added to the consensus sequence, however it extends beyond the region of the trimmed sequence. We will need to shorten it on both ends. Zoom in on the sequence using the Magnifying glass "+" button, and scroll to the left end of the sequence.
+
+Drag the end of the annotation so that it lines up with the end of the trimmed consensus sequence.
+
+.. figure:: /images/annotation_before_drag.png
+  :align: center
+  :target: /en/latest/_images/annotation_before_drag.png
+
+The left end of the annotation should now look like this:
+
+.. figure:: /images/annotation_after_drag.png
+  :align: center
+  :target: /en/latest/_images/annotation_after_drag.png
+
+Repeat the annotation trimming procedure on the right side.
+
+Finally, click the Save button to save this Annotation.
+
+Submitting Annotated Sequences to GenBank
+-----------------------------------------
+
+Make sure to follow this manual annotation procedure for all of the ITS sequences you will be submitting to GenBank.
+
+To submit to GenBank, follow the same procedure detailed here: http://bwp-informatics.readthedocs.org/en/latest/gb_upload.html, with the following changes:
+
+- In the "Field Mapping" section, Genetic Location should be "Genomic"
+- Rather than selecting "Add Gene & CDS features using fields", select the option above it: "Include Features/Annotations". This will ensure the ITS Annotation you just added will be submitted with the sequence. Make sure that "Also include annotations in tracks" is NOT selected.
+- In the Traces tab, select "TARGETED LOCUS" for "Experimental Strategy". All other selections will stay the same.